Last year's system was deffinetly a problem for a lot of people. For whatever reason the tickets in your cart weren't held for you until you 100% checked out. As someone said before, you could be in the process of purchasing the tickets and someone else if they were faster would buy them from under you.
I would strongly suggest having your card and info loaded into Flash Seats before you even go into the waiting room. If i recall correctly they allow Apple Pay, so that makes the whole process take 5 seconds.