This happens on Krita 3.0.1 and 3.0.1.1 64bit version, have not tried others.

When you have a very large image with many layers, it seems like all transformation options that go through each layer (such as resize, transforming a group, cropping, etc) get stuck if there is an empty layer. The process will get stuck on the empty layer, and won't complete - I tried waiting for around 10 minutes, it stayed at 0%. You cannot cancel the transformation either, and you can't save, because the program is waiting for the transformation to complete - but you can't stop it. Leads to a lot of headache and lost work.

It's possible that this happens on small resolutions and with few layers as well, but I didn't get around to testing it. And for what it's worth, I think all the layers that caused this were pasted from another file, and the contents deleted with delete thereafter.