Texture resolution mismatches causing blurriness/aliasing, floating point errors and bad level design causing collision detection problems (getting stuck in the walls), frame rate and other update rates not being synced causing stutter and lag (and more collision detection problems), bad illumination parameters ruining the look they were going for, numeric overflow breaking everything, bad approximations of constants also breaking everything somewhere eventually, messy model mesh geometry causing glitches in texturing, lighting, animation, collision, etc.

There's probably a lot more I'm not thinking of. They have nothing to do "with the hardware", but the underlying math and logic.

They're also not bugs to "let the programmer figure out". Good programmers and designers work together to solve them. I could just as easily hate on the many criminally ugly, awkward, and plain unfun games made by programmers working alone, but I'll let someone else do that. :)