When an opponent plays a card that gets triggered over 100 times due to copy effects, this particular card put copies of another into the deck and has a longer animation that has to play over 100 times before anyone can even choose another input. The timeout timer went through all of their time outs, and then started taking my timeouts while I had no option to choose anything. By the time the animation has finished, it's already passed my turn with warning that I'm about to be kicked from the match and then my opponent gets an entire extra turn.
Seems like to me if the opponent has a long broken combo and they run out of a timer, then it should immediately end anything on the stack and then the next player gets to go.