For example, Ctrl-w is a very important keybinding on IDEA, one that I use all the time (it expands the selection to the enclosing expression). It's literally wired in my brain now. To the point that I now use it in Eclipse as well and I even started using it in other places (Sublime, etc...) and... closing the window as a result. Very annoying.
Another one is that Ctrl-n sometimes creates a new file (expected) and sometimes... something completely different depending on your current window. Again, not friendly. Optimized for development and a life saver on the long run, for sure, but it's fairly user hostile.