mapping warning: deviates by more than 1.0 (tolerance)

Hi, I've been doing a few tests with openfe recently and I think it's a really cool and useful tool for running free energy calculations. Thanks! But when I create networks and build hybrid things between below two molecules, I see some warning msgs (e.g., WARNING: mapping 13 : 1260 deviates by more than 1.0), even if these two molecules are in great alignment. I'm not sure if I can ignore these warnings.

Also, I digged into the source code and found that 1.) the positions of core atoms are copied from ligA and then copied from ligB (_compute_hybrid_positions is just assuming that the positions of cores are same in ligA and ligB.); 2.) the positions of unique atoms in ligA is just copied from ligA; 3.) the positions of unique atoms in ligB is just copied from ligB. Not sure if it's reasonable. What if there's a small shift between ligA and ligB?

Another question is I also saw this warning: UserWarning: atom_indices are not monotonically increasing warnings.warn('atom_indices are not monotonically increasing') Not sure what's going on here. I'd appreciate it if you have any thoughts.

FYI, I attached a few files:
conda env: environment.yml
my code and output: run.ipynb
ligands: ligands.sdf
hybrid_system.pdb was generated from the test.
files.zip