Here's a couple of more that I remember.

When I was in college (back in the early 1980's), we were programming on a mainframe computer. When you compiled a program, it would generate a compile listing, which would contain the source of your program along with error messages. The compile listing would be displayed within the text editor. (You can see what's coming, can't you?) On more than one occassion, I would be looking at the compile listing, see my problem, make the correction to the source within the compile listing, and then be mystified as to why the problem was still there when I recompiled.

The other one that I remember involved setting some values in a hash, then trying to retrieve those values and coming up empty. The problem was, when the values were being set, the keys were ALL-CAPS, but when we were retrieving them, the keys were lower-case. I was pair-programming with someone and to this day, whenever we make a bone-headed programming mistake, we look at each other and say "Hashes are case sensitive!"