I'm seeing the AP bars pulse in PVP matches (so no goons). I don't think I'm being mistakenly credited with any AP though.
It seems to happen after the enemy team makes a match: first one AP bar would flash for the AP they gained, then the yellow, red, and black AP bars for both teams would pulse with no changes. If there are multiple AP changes during the enemy turn, I see this yellow/red/black pulse after each one.