I've had this happen to me several times as well. I think it usually happens when I'm playing international opponents. I wonder if it has something to do with compensating for lag in the interweb.
issue with blitz timing
Its premove and lag. The opponent makes a move on your time (premove) which is legit so it doesn't take any time off of his clock, but you see his time run down on your end due to lag (either his, yours or both)

may also be premove and lag, of course.
//edit: So I agree with Phaethon, who was faster than me :-)

I have been in a winning position time wize and after my move their time jumped up 5-6 seconds! most annoying especially in bullet
This has happened to me in two separate games with 2 minutes per side. In the first game, my opponent had 5.2 seconds left, them thought for about a second, then made his move and the timer went back to 5.2. This happened about 5 times, then I lost, but I should have won on time. In the other game the same thing happened, but he had 1.3 seconds. He made about 5 moves, and I should have won on time after 2 of them. I'm not sure if there is a reason for this or anything, but I'm just saying.