Not my bug and not CS, but I think that the most-difficult bug(s) I've read about is the American Mark 14 torpedo in World War II. A combination of constrained budget for testing before the war, extreme inability to meet supply (and thus provide some for testing), difficulties in observing the things in production in operation (it's a torpedo, and the target probably isn't too amenable to you looking at the thing if it doesn't work well), secrecy, cutting-edge technology, and several other problems, a number of modes of operation (including both a contact and proximity magnetic fuze), and including multiple bugs that had a tendency to mask or affect each other, including specifically:

• A tendency to run deeper than set (and sometimes go too deep and not hit or detect a ship)

• A tendency to bend a critical pin on impact if the torpedo impacted a ship at something like right angles, but not at an angle; if bent, the torpedo would not detonate.

• Testing that happened in the Atlantic, but with most use in the Pacific. It turns out that Earth's magnetic field is not uniform, and varies enough to throw off magnetic fuzes and cause premature explosions or non-explosions.

...led to the US fighting a war that was heavily-naval, where the main weapon for sinking major ships was the torpedo...but where that torpedo wasn't really very functional for something like 18 months of fighting.

Wikipedia has a somewhat longer version.

This long explanation is probably the best I've read.