I too have had this problem since the patch. To the point where I am almost ready to open up the editor and tone down the injury frequencies myself! The biggest cause in my save I think is that I need the pitch relaid. Been starting a first XI with no lower than 98% conditioning at mid-season fitness and still carting off 2-3 every game with injuries. Seems like mine are not usually the long term ones other people are having issues with, but it sure is frustrating to never be able to make a tactical change during a game because I have so many injuries.
As far as training I have them resting before and after a match, changing week focuses often. I only ever train fitness on weeks with one or fewer games. Should I be training this more often to avoid injuries? Counter-intuitive but I may experiement.
It does not seem to correlate to specific players always getting injured. I have noticed it is typically my CM's and CD's that get carted off (thankfully not my ST or wing players as I don't have much depth there). Is there something buried in player instructions that could be adjusted to limit them from dangerous situations that leave them injured? Tackling Style, agression, or others perhaps?