The big one I remember was many applications, not just games assuming the buffer swap was performed by a blit into the display buffer, not an framebuffer pointer update. They relied on the previous frames data still being in the back buffer. For those applications you were forced to blit the buffer, not swap the pointer and take a performance hit.
I also remember a media player being called out by name in the code for doing invalid operations, needing a work around and code to detect it was running just to function.
Rapid Chip Reverse Engineering Using Laser, Focused ion beams, and Scanning electron microscope https://academic.oup.com/mam/article/30/Supplement_1/ozae044...
FIBs are also used to test modifications before doing a respin. I'm still in awe that matter can be manipulated so precisely