I just had the exact same problem. Opponent was in an infinite draw loop and somehow the game started using my timeouts, even though I had already clicked through to accept all and not respond.

Same issue here. It's complete BS! I had over 200 creatures and because of my opponents stacking ability with +1/+1 counters triggered for each of my creatures, this issue cause me to timeout some how. It even caused me to drop a rank. Completely unfair. I could only imagine if this was a tournament with a cash prize at stake. I shouldn't have been decreased a rank!

Same here. Opponent stacked a lot of abilities, and while they were "auto" resolving i timed out, then loose the game at the beginning of my turn. I shouldn't have lost any time while my opponent was playing.

Same here. Opponent flooded the stack with triggers, I had no priority to pass, so opponent should have eventually timed out. But instead I TIMED OUT. And when brought to WotC Customer Support attention, they replied that maybe my device doesn't meet the minimum specifications. Are you kidding me? I have a device Arena mobile-compatible since day 1!!! They cannot even admit that they are giving us a bugged product, that is ridiculous considering it should be a """STABLE""" release and not an alpha/beta release!!!

Your opponent's stacking ability is over 100, and your opponent clicks on a creature each time to put a + 1 / + 1 counter on it. The other party's time should have been consumed, but my time was consumed and I lost the timeout.