If you are using the latest (July 2022) C36 port, we have included basically the whole force field, which means more terminal patches that might or might not be relevant. pdb2gmx is matching “MET” from the protein sequence with a terminal patch that should only be applied to carbohydrates. This is something that pdb2gmx tries to be smart about but sometimes fails.
The solution is to manually select appropriate terminal patches with the -ter option.