ukemi does not always save you
My long term injuries are a result of my partner doing something that I could not avoid. My elbows are permanently painful. Both elbow problems were caused by my partner's lack of sensitivity when I was pinned, causing overextension of the elbow joint.
Both original injuries were caused by experienced aikidoka and by that I mean at least 4th Dan but has happened so many times since that I have to stop training on elbow techniques after just a few (for instance hijiate & hijishime).
Two weeks ago it was a 1st kyu. I was pinned on the floor and he messed up my elbow again.
Other than not training, I can't see how I will stop this happening other than never train with someone I don't know very very well.