Click on the ball and give the open command in the bottom right. It's like a switch or anything else. If a pawn isn't opening it, right click and force it.

if the thing @Lotaxi said doesn't work then it might be because other mods are incompatible. Maybe try removing mods that affect how animals work in the game like giddy-up or that mod that makes animals work harder.

Thanks for the responses! I'll try those out.

It worked after I disabled the mods "Dinosauria" and "Alpha Animals". I am also running the game with 100% pokemon replacement, so that may also be a factor in why it didn't work. Hope this helps anyone else.

Hmm I'm having the same issue with Alpha Animals enabled. I liked the idea of having Pokemon alongside my usual crazy Alpha Animals wildlife, but maybe that's not possible at the moment?

Update: the conflict was with GiddyUp Ride and Roll. Removed that, while still using Alpha Animals, and I can now open the Pokeball.

For info, this issue has been fixed in the latest update