How to avoid the appearance of extra hydrogens from lattice packing of PDB file?
This is a bug, which is clear.

My guess is that you don't get $\ce{CH6}$ but that there's some disorder, so the transformations put two near-identical $\ce{CH3}$ groups on top of each other. Thus, one C becomes two, and each gains hydrogens.

There's usually a "slop" factor to detect near-equivalent atoms, but it's clearly failing.