For the tokens, when I was testing manifest, I was using a fresh game folder. Nothing in it except for the cards explicitly used in the test deck which included nothing token related EXCEPT my test card Favor of the Gods. When I used manual mana from it, the crashed. That would have been an event of tokens leaving the battlefield, so it still matches up with the other problems. It's not token registrations. (I've checked the test card multiple times. It has registrations for all five colors and colorless.) And I know it's not a problem in the functions (if it was, then the crash would have happened when making the tokens, not when using their mana ability). That leaves something in the engine not behaving properly with token leaving the battlefield.
However, sometimes, tokens NEVER cause problems. I used
Flamewright in a deck and made over a hundred tokens from it, including a large number from copies of
Flamewright. I exiled, destroyed, and bounced various numbers of them all at once or individually and never had a single issue with it.
In other instances, one token by itself can cause a problem. I often have trouble with manual mana tokens (not because they're more susceptible, but rather, I suspect, simply because I deal with them a LOT more often than I deal with any other particular type of token).
One thing i was wondering is if perhaps the token registrations are messed up in a way I'm not aware of. For instance, does the "registration"
always need to be 1, or should it increment? Should it start at one and count up for each new registration? (One card did this, but I didn't think anything of it, I just changed them all to 1). If that's the problem, then the manual mana from my test card would make a lot of sense since they all use the same registration register and
Flamewright would never have had an issue because there's only one token produced by that card. I don't think that's the problem, but it's a possibility. There are a couple other things that could potentially be the problem, but there are only so many things that could cause this kind of issue.
Anyway, I'll go look into this and see if I can find a reliable way to crash the game with tokens and then find a way to stop the crashing.