I have been seeing this since the release of Pixelmator Pro...and I was hoping it would be addressed/fixed by now. This morning I have wasted a solid 45 minutes trying to merge layers, unsuccessfully. This is unacceptable from a $60 photo editing program!
Is something not working like it should? Let us know.
Sorry to hear you're having these frustrating issues! We do know things like this can sometimes happen although the exact steps to recreate them have been a little tricky to pin down — to help us get to the bottom of this, it would be awesome if you could share the PXD file with us at email@example.com. If you'd rather not do that, are there any specific circumstances (or steps) that make this bug appear?