Outputs % / percent sign after every command in some panes

Just installed and playing around with a configuration. Running in gnome terminal with zsh and tmux.
This is the configuration of the 1st window where issue appears:

session_name: OMG
start_directory: /home/pj
windows:
- focus: 'true'
  layout: 814f,190x48,0,0{95x48,0,0,0,94x48,96,0[94x24,96,0,1,94x23,96,25,2]}
  options:
    automatic-rename: 'off'
    monitor-activity: 'off'
    remain-on-exit: 'on'
  panes:
  - focus: 'true'
    shell_command:
    - l.
  - screenfetch
  - fortune | cowsay
  window_name: TERM

The issue is, when starting tmux session with "tmuxp load OMG" the 1st and 2nd pane display "%" after each issues command. Happens when the session is loaded with "l." and "screenfetch" and for every command issues afterward.
Strangely the 3rd pane issuing shell_command: "fortune | cowsay" doesn't display "%" after the command, nor after any next command.

This doesn't occur ever if I start tmux manually in any pane or any window. It is possible to kill the troublesome panes and create new splits and the issue is gone. But that nullifies tmuxp's benefits if I have to remake whole 1st window everytime I open this session.

Any ideas why this would occur?

Example is displayed in this https://s14.postimg.org/ul2tnsu75/tmuxp_Issue_Screenshot_from_2018-03-13_19-28-23.png.

Information about my system:
Python version:
python --version Python 2.7.13
python3 --version Python 3.5.3 (installed using pip3)
system PATH:
echo $PATH /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/sbin/:/home/pj/bin/:/home/pj/Applications/cava/:/home/pj/.local/bin/:/sbin/:/home/pj/bin/:/home/pj/Applications/c ava/:/home/pj/.local/bin/ (after seeing this I realized my /etc/zsh/zshenv gets sourced twice? This is the troubling line: export PATH=$PATH:/sbin/:$HOME/bin/:$HOME/Applications/cava/:$HOME/.local/bin/, but I don't think this is causing my issue.
tmux version:
tmux -V tmux 2.3
tmuxp version:
tmuxp --version tmuxp 1.4.0
tmux path:
which tmux tmux: aliased to _zsh_tmux_plugin_run
tmuxp path:
/home/pj/.local/bin//tmuxp (I have no idea what's wrong with "//" here. tmuxp executable is located in the /home/pj/.local/bin/ directory)
libtmux version:
can't find libtmux.
shell:
chsh Login Shell [/usr/bin/zsh]:
output of tmux list-sessions:
tls OMG: 5 windows (created Tue Mar 13 19:48:30 2018) [171x42] (attached) XXX: 5 windows (created Tue Mar 13 19:24:28 2018) [171x42] (XXX is the manually fixed version I keep running with resurrect and continuum tmp plugins)
tmux list-windows:

`tmux list-windows
1: TERM*M (3 panes) [171x42] [layout 5742,171x42,0,0{85x42,0,0,38,85x42,86,0[85x21,86,0,39,85x20,86,22,40]}] @19 (active)
2: SYS (2 panes) [171x42] [layout 987f,171x42,0,0{112x42,0,0,41,58x42,113,0,42}] @20
3: CMUS (2 panes) [171x42] [layout 9882,171x42,0,0{112x42,0,0,43,58x42,113,0,44}] @21
4: WMON (2 panes) [171x42] [layout 9885,171x42,0,0{112x42,0,0,45,58x42,113,0,46}] @22
5: MC- (2 panes) [171x42] [layout 9888,171x42,0,0{112x42,0,0,47,58x42,113,0,48}] @23

tmux list-panes:

tmux list-panes 
1: [85x42] [history 1/20000, 43 bytes] %38
2: [85x21] [history 4/20000, 460 bytes] %39
3: [85x20] [history 2/20000, 146 bytes] %40 (active)

output of tmux show-options -g:

tmux show-options -g                                                                                                                                             
@batt_remain_short "true"                                                                                                                                                  
@continuum-boot "on"                                                                                                                                                       
@continuum-restore "on"                                                                                                                                                    
@continuum-save-last-timestamp "1520967267"                                                                                                                                
@plugin "tmux-plugins/tmux-battery"                                                                                                                                        
@resurrect-restore-script-path "/home/pj/.tmux/plugins/tmux-resurrect/scripts/restore.sh"                                                                                  
@resurrect-save-script-path "/home/pj/.tmux/plugins/tmux-resurrect/scripts/save.sh"                                                                                        
@resurrect-strategy-irb "default_strategy"                                                                                                                                 
assume-paste-time 1                                                                                                                                                        
base-index 1                                                                                                                                                               
bell-action none                                                                                                                                                           
bell-on-alert off                                                                                                                                                          
default-command ""                                                                                                                                                         
default-shell "/usr/bin/zsh"                                                                                                                                               
destroy-unattached off                                                                                                                                                     
detach-on-destroy on                                                                                                                                                       
display-panes-active-colour blue
display-panes-colour brightred
display-panes-time 1000
display-time 750
history-limit 20000
key-table "root"
lock-after-time 1800
lock-command "lock -np"
message-command-style fg=yellow,bg=black
message-style fg=brightred,bg=black
mouse on
prefix C-b
prefix2 C-a
renumber-windows on
repeat-time 220
set-remain-on-exit on
set-titles on
set-titles-string "#T - #W"
status on
status-interval 2
status-justify left
status-keys vi
status-left "#{?client_prefix,#[fg=colour254]#[bg=colour31]#[bold]#[noitalics]#[nounderscore],#[fg=colour16]#[bg=colour254]#[bold]#[noitalics]#[nounderscore]} #S #{?client_prefix,#[fg=colour31],#[fg=colour254]}#[bg=colour233]#[nobold] #(env $POWERLINE_COMMAND $POWERLINE_COMMAND_ARGS tmux left --width=`tmux display -p '#{client_width}'` -Rwidth_adjust=`tmux show-options -g stat
us-right-length | cut -d' ' -f2` -R pane_id="`tmux display -p '#D'`")"
status-left-length 20
status-left-style default
status-position bottom
status-right "#(/home/pj/.tmux/plugins/tmux-continuum/scripts/continuum_save.sh)#(env "$POWERLINE_COMMAND" $POWERLINE_COMMAND_ARGS tmux right -R pane_id="`tmux display -p"#D"`" --width=`tmux
 display -p "#{client_width}"` -R width_adjust=`tmux show-options -g status-left-length | cut -d" " -f 2`)#(/home/pj/.tmux/plugins/tmux-cpu/scripts/cpu_bg_color.sh) CPU:#(/home/pj/.tmux/plug
ins/tmux-cpu/scripts/cpu_percentage.sh) #(/home/pj/.tmux/plugins/tmux-battery/scripts/battery_status_bg.sh) #(/home/pj/.tmux/plugins/tmux-battery/scripts/battery_icon.sh)#(/home/pj/.tmux/plu
gins/tmux-battery/scripts/battery_percentage.sh)"
status-right-length 150
status-right-style default
status-style fg=yellow,bg=black
update-environment "DISPLAY SSH_ASKPASS SSH_AUTH_SOCK SSH_AGENT_PID SSH_CONNECTION WINDOWID XAUTHORITY"
visual-activity on
visual-bell off
visual-silence off
word-separators " -_@"

tmux show-window-options -g:

tmux show-window-options -g
aggressive-resize on
allow-rename on
alternate-screen on
automatic-rename off
automatic-rename-format "#{?pane_in_mode,[tmux],#{pane_current_command}}#{?pane_dead,[dead],}"
clock-mode-colour green
clock-mode-style 24
force-height 0
force-width 0
main-pane-height 24
main-pane-width 80
mode-keys vi
mode-style fg=black,bg=yellow
monitor-activity on
monitor-silence 0
other-pane-height 0
other-pane-width 0
pane-active-border-style fg=brightgreen
pane-base-index 1
pane-border-format "#{?pane_active,#[reverse],}#{pane_index}#[default] "#{pane_title}""
pane-border-status off
pane-border-style fg=black
remain-on-exit on
synchronize-panes off
window-active-style default
window-style default
window-status-activity-style fg=colour11,bg=colour233
window-status-bell-style fg=black,bg=red
window-status-current-format "#[fg=colour233,bg=colour31,nobold,noitalics,nounderscore] #[fg=colour117,bg=colour31,nobold,noitalics,nounderscore]#I#F  #[fg=colour231,bg=colour31,bold,noitalics,nounderscore]#W #[fg=colour31,bg=colour233,nobold,noitalics,nounderscore] "
window-status-current-style fg=brightred
window-status-format "#[fg=colour244,bg=colour233,nobold,noitalics,nounderscore]  #I#F #[fg=colour240,bg=colour233,nobold,noitalics,nounderscore] #[default]#W   "
window-status-last-style fg=colour31,bg=colour233
window-status-separator " "
window-status-style fg=brightblue
wrap-search on
xterm-keys on

uname -a
Linux debian 4.9.0-5-amd64 #1 SMP Debian 4.9.65-3+deb9u2 (2018-01-04) x86_64 GNU/Linux
gnome-shell --version
GNOME Shell 3.22.3
gnome-terminal --version
GNOME Terminal 3.22.2 Using VTE version 0.46.1 +GNUTLS
zsh --version
zsh 5.3.1 (x86_64-debian-linux-gnu)

Within tmux: echo $TERM
screen-256color (it's set in .tmux.conf)
Outside tmux in zsh: xterm-256color

Sorry about this. It's more than I'd wish to paste...

I assume it's some kind of TERM issue that gets lost within Oh-My-Zsh configuration. But the thing is this "%" only apears when I load tmuxp session.

Any ideas?

Start with the supplied YAML session configuration and the tmuxp load OMG entry point; reproduce the percent signs in panes running l. and screenfetch, then compare them with manually created panes. Use the reported tmux, zsh, TERM, and tmuxp versions to isolate the behavior; done means a reproducible cause and a verified fix or documented limitation.