The most annoying bug for me is the scoring bug. A drawn game is scored as a win for one side instead of as a draw. (Draws are most common in rulesets which allow integer komi, but can also happen under Japanese rules, e.g. in the case of triple ko. Rulesets which don’t completely prohibit repetition of the position, i.e. only prohibit the simplest case - immediate recapture of a ko - allow indefinite repetition in a variety of ways, though they rarely occur in practice.)