I don't know how these are called in ToT, so using the MTG term "zone".
There are at least two bugs I have been able to consistently reproduce related to cards changing zones:
1) If I refresh a card with Combo, then draw it, its Combos do not trigger based on previously played cards. Especially noticeable when I refresh then draw Wispheart Totem that has Combos 2, 3 and 4, then play it, and only get the "face value" effect despite having played half a dozen other Druid King cards that turn.
2) Sacrificed cards don't seem to count towards combos, either. E.g., if I play Customs Seizure, then use the Grandmaster Delmene Hlaalu patron ability to sacrifice it, then subsequently play Hireling, its Combo 2 ability does not trigger.
I am not sure if it's happening with every single card, but the above examples are 100% consistent.