Issue when removing overlaps in Glyphs 3

I use Glyphs since ever but since the last upgrade I’m experiencing something new: Problems exporting the fonts due to Remove Overlap issues. I’m posting 2 images to show what’s happening and hope you can help. BTW: All the paths are with correct directions, but all the time the nodes don’t align (like the top serif of the Be-cy) it gives this issue.

The path direction is wrong.

Thanks. I will, check that.