Created attachment 106149 [details] Video showing this bug. After cropping an image that has vector layers and closing the file, vector layers are in wrong place after opening the file again. Possibly it's just the old position but relative to the new beggining?. Trying to fix that by moving the layers to the spot they should be at, and saving again, moves them even further.
Yes, I can confirm this behaviour (Krita 4.0.0 pre-alpha on Ubuntu 14.04).
I've noticed that Wolthera report is later, however it contemplates also a couple of related issues. For this reason I'd track Bug 381944 from now on. Feel free change the status back. Thanks *** This bug has been marked as a duplicate of bug 381944 ***