So in this scenario there's a general case and a special case.
The general case is where merging a patch makes the code invalid in some sense. This can range from a syntax error to a subtle bug. Version control systems don't prevent this, because they can't: in full generality, correctness is an opinion of the author.
The special case is where two patches each create a valid program, but applying both of them makes the program invalid. I think that's in the FAQ because pijul makes much of the fact that it has a sound theory of patches, as it should, that's a wonderful thing. But people commonly confuse soundness and validity, leading to questions like "so what you're saying is that a merge will never result in a borked program?".
IMHO that shouldn't be in the FAQ though, because it creates the impression you got, which is that Pijul is talking about something which might be possible in principle but which it doesn't happen to be capable of. It's just patiently explaining that Pijul can't do impossible things.