Hey Specialist, my thoughts on longer term injuries...
Are they a result of overcompensating for an underlying injury/issue elsewhere? Compensating by using other muscle groups etc in lieu of the injured muscle and aggravating everything else because of the way you are now loading your body?
Are they the result of part of your body be relatively stronger than another part of your body and this imbalance - see this in people who stick to the same exercise routine and don't very it. Also leads to overcompensation because your strong muscles take over everything.
Misdiagnosis - injury that is not diagnosed correctly may not be getting better and causing other issues. I had a massive crash earlier this year on my XC bike cracked a couple of ribs, right knee was in a bad way and left shoulder. Broken ribs not much you can do about them, was cleared of a broken patella and was told no rotator cuff damage (which I knew as I did the stretches for that straight after the crash). Over the next couple of months I saw a couple of different doctors and got the 'muscle/tendon strain/soft tissue - will clear up with rest'. After 4 months I insisted an ultra sound was done - and then saw a good doctor who before looking at the ultra sound listened to my story and asked me to do a couple of stretches. Did the rotator cuff ones and then he asked me to do a different exercise and 'bang' that exercise perfectly isolated the issue. He said 'bursitis' looked at the report 'yep bursitis' and prescribed treatment - shoulder is improving greatly and hope to be back on on downhill bike in about 4 weeks.
I guess the underlying point of the above comments is if you are having ongoing issues you need to change something - I think to do this effectively you will need an external input whether it is a physio, trainer, GP, sports injury doctor but you need somebody to look at you and give you some feedback.
"Insanity is doing the same thing over and over and expecting different results."