Alright, two things happened:
1. I slipped into a shop and the graphics glitch followed me, exactly as it appeared in the picture. As in, it didn't refresh or start over, but remained exactly as it looked in town. Difference was that a bomb started charging and exploded. I guess the bombs are prevented from spawning in town, but the shop isn't considered "in town" by the aura.
2. When I left the town, things started behaving as expected.
I would recommend not having the countdown start until you have left town. Don't want to be planting a bomb just as you enter a new region.