Thanks for the clarification, friend!
Plenty of things seem off here. While the card says "Up to 2" in reality, the effect can't be played without targets (This is going to be fixed in version 0.4.1), so for starters, you shouldn't be allowed to do that.
Edit: I just realized, but rather than the situation below, it's likely to be a problem where your cards got milled, and then you tried to use the Exhume effect on the milled cards, which in version 0.4.0 causes a game freeze! This is already fixed in the new version which will be released sometime next week.
Not having cards in deck should have no impact on the Exhume effect, however, what I'm thinking could've been a problem in this version is your opponent's "Gain control of target Minion" ability. Could it be that your opponent stole one of your Minions, then it died, and then you tried to Exhume that same Minion?
At any rate, I've been working on the code for playing cards to fix some issues so hopefully this won't happen in the next update even if I can't reproduce your situation exactly.
Again, thanks for the feedback, it's very helpful!