I've noticed that happen many times in the past and I don't understand why. Of course, I've never bothered to look it up, but I though the rule about going out of bounds was pretty cut and dry.
The clock stops for just a brief moment when a player goes out of bounds with the ball and begins running again as soon as the refs spot the ball. The exceptions to this rule are (1) with 2:00 or less in the first half and (2) with 5:00 or less in the 2nd half.
That has been the rule for more than 10 years, people. The NFL instituted the change to try and reduce the amount of time games took.