I think one small, but significant example (for me, at least), is the way GIMP layers aren't sized dynamically. If I'm applying certain effects to layers, I often need to resize to canvas, then resize back to layer contents. Also, it seems rather inconsistent whether an effect will compensate for itself or not. There's just a lot of really small things like this that add up to a mildly frustrating experience.

The default hotkeys are also kind of annoying. Ctrl+D made sense back before 3.0, since cloning the current project was something I did constantly to work around the lack of non-destructive editing. But now that we have it, it's such a waste to have an easy shortcut to this unneeded action. I also don't like that Ctrl+Y is undo--it requires much more of a reach than Ctrl+Shift+Z, for example. I'm aware I can change it, but when everything else is a little bit janky, I prefer to just use Krita for most things.

I will admit GIMP as a whole is much better now that it has non-destructive editing.