Hi @goncaloveigacl, welcome to the forum!
The error happens when you try to add windows to an underground wall. It should not happen with this sample model. What are the numbers that you are using for projection distance and angle tolerance when you try to add the windows to the model? I suspect you might be using a very large number, and Pollination is trying to add the skylights to the ground floor.
If that’s not the case, then try to run the Auto top-ground command and set the Basement count to 0.
Then try adding the windows again.
Let me know if this resolves the issue.