Either way it's still caused by there being NONE monster IDs in the list of enemies to fight. Weird.
I had a little dig in the codebase and I think I have another idea for what could cause this. The code that checks for valid monsters to send out only checks if HP > 0. If the matching AMP ID's amp_MONID is NONE then we have an invalid monster ID and reading data from that will cause issues.
Do you set up / clear data for totems properly (similar to how the engine handles enemy data in random encounters)? It feels like there might be something going on with partially initialized data that causes this.
One idea might be to extend battle_get_valid_reinforcements a bit so that line 6 checks this condition instead:
if(global.active_monster_party[mon,amp_HP] > 0 && global.active_monster_party[mon,amp_MONID] != NONE){
It's not fixing the core issue that causes the invalid data but it at least stops trying to spawn a nonexistant monster. Maybe it'll be enough, since most other AMP manipulation scripts checks if the monster ID is NONE to check if a slot is valid.