It may have looked that way since you can't see the tenths that continued to run off, but we know the clock continued to run by watching the next play.
It changed to 2:00 within 1-tenth of a second on the next play which means that 9-tenths ran off of 2:01. The Jets player first touched the ball at the end of 2:02:
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That leaves a full second to determine possession and stop the clock. Do extra seconds run off the clock sometimes when they should not? Probably, but that doesn't mean they should and that we should expect them to all of the time. You see PI that does not get called all the time, but that doesn't mean you get screwed when you do commit PI and it does get called.