Tunrs out the problem was caused by either mod caching or multithread loading. I still don't know what really caused it, but turning these on and off helped me.

Sounds crazy, the tokens are implemented as normal. There is no negative index and I do not have this issue.

The ones that should be in the top left corner, right below the chest.

What player meeples do you mean?

For some reason the game cannot import the player meeples. It sais: Error creating Token Mesh: Index was out of range. Must be non-negative and less than the size of the collection. Parameter name: index