That happens frequently, it's only progressing one sub-pulse and then something interrupts the increment. I'm assuming you don't have any messages in your log that would indicate the cause. Check for missile fire controls left active without a target. Otherwise it's probably a situation like an NPR detecting another NPR somewhere after jumping through a JP, deciding to jump back through to flee, forgetting they exist and jumping back in, detecting them once more and causing an interrupt every time. In that case you're going to need to edit the DB or enter designer mode to locate and fix the problem (by deleting one of the offending ships/fleets), but with that you need to know what you're doing to some degree and Steve doesn't like it, so don't post anything as a bug from that DB thereafter.
Probably you have NPRs shooting at each other. The best solution is usually to set the game to auto turns and click the 5 minute turns button, then browse the forums for a couple minutes until the combat finishes.
If they're shooting each other the increments should get reduced in time and there should be a message in the log about it.