I had seen this problem a few times before but only figured out the cause now.
So the goons will have two countdown tiles out, a 2 turn and a 1 turn. The 2 turn tile is above the 1 turn tile. Since the countdowns are resolved in a set order (top left to bottom right), the 2 turn countdown will go to 1. Then the 1 turn countdown will go off. Now, the AI will continue looking for countdown tiles from the location that the one went off from. If a countdown tile started above that location, but is now below, it will have a second turn removed from the timer.
If this doesn’t make sense, let me know and I will try to be more clear.