Input bug on Retroarch Flatpak

First and foremost consider this:

• Only RetroArch bugs should be filed here. Not core bugs or game bugs
• This is not a forum or a help section, this is strictly developer oriented

Description

(First of all, I'm spanish and I'm not that fluent in english. I may have some grammar errors, I'm sorry if I'm not explaining myself as clear as I should)
Retroarch Flatpak missdetects input in very bothering ways.

Expected behavior

Normally and with Appimage and DEB versions, I plug the controller in, and it works perfectly, no bugs at all.

Actual behavior

Whenever I plug my controller, the program does very weird things, like start scrolling up in the menu even if I'm not pressing anything, or gets stucked into the first direction I pull the joystick (for example, if it starts and I press down in the menu, then no other direction works). I am pretty sure it's not the controller because I have tested it with other controllers, I am also sure it is not my computer because Appimage works well and DEB is ok too.

Steps to reproduce the bug

1. Start Retroarch
2. Plug the controller
3. Press any joystick
4. It starts to do one of both things I told before

Bisect Results

It started at the last update, I think it was 1.16. I am not 100% sure, but I think I read this update comes with an input error correction. Maybe this correction caused it, I have no idea.

Version/Commit

(It happened also with Fedora 39)
Operating System: Debian GNU/Linux 12
KDE Plasma Version: 5.27.5
KDE Frameworks Version: 5.103.0
Qt Version: 5.15.8
Kernel Version: 6.1.0-17-amd64 (64-bit)
Graphics Platform: Wayland
Processors: 4 × Intel® Core™ i5-3470 CPU @ 3.20GHz
Memory: 7.6 GiB of RAM
Graphics Processor: Mesa Intel® HD Graphics 2500
Manufacturer: Hewlett-Packard
Product Name: HP Compaq Elite 8300 SFF

• RetroArch: [version/commit]

Retroarch 1.16.0.3

• OS: Linux Debian 12
• Compiler: Flathub

Start by reproducing the controller behavior in the Flathub RetroArch 1.16.0.3 build using the listed steps, then compare it with the working AppImage and DEB versions. Done means plugging in the controller no longer causes menu scrolling or leaves joystick input stuck in one direction.