My first real injury in Aikido was a straining a ligament in my knee. I'd been hurt before, but this was the first time I had to visit the doctor and was off the mat for an extended period of time (2 months no practice, 6 months light practice).
I over-extended myself while attacking my Sempai during a tski kota gaeshi. We practice on the standard blue excercise/tumbling mats, which can be sticky and very spongy. When my Sempai performed the kota gaeshi, my upper body turned, but my foot remained planted. I strained one fo the ligaments in my knee. (This really sucked because I still had to drive my stick shift truck 20 miles home from the dojo.
I've had a few other actual injuries requiring medical attention, including a partially separated shoulder. But, they are starting to become much less frequent as I become a better uke and learn to break fall out of almost anything.