I know there are some Genesis games that, even unmodded, have a bad checksum.
Not sure if anyone has bothered to make a list.
Retrode has noted Blaster Master 2 as one example.
I can't recall if Zero Wing has a "bad" checksum (as I know both regions have the effective ROM size wrong in the header). (that is, if the checksum matches either the wrong 512KB size or correct 1MB size.)
MegaPanel is another I know, as I have personally dumped my cart a few times to check, even tried overdumping it with the same result.