Occasionally (but often enough to be annoying), the RMB will mark a square instead of tagging it with an 'X'. I've had it happen when individually tagging a square and also when dragging across multiple squares, where the first square will be marked but the rest in the sequence get tagged with an 'X' like intended.

Like I say, it's annoying but if you're not paying attention to what the game is doing, you can overlook the switch altogether only for the mistake to catch up with you later in the puzzle.