I can only speak from my own personal experience, although I think I was at a similar stage to yourself a few months back - and getting pretty frustrated by niggly injuries. I would say if you do have these sorts of injuries it is definitely worth getting some gait anlysis to check for any problems - for me heavy overpronation was part of the cause of these injuries when the distances I was running increased.
I would say it is you must listen to your body, and just take a couple of days off if something concerns you, and take it easier just in case the injury becomes more serious. I find it difficult sstill to distinguish between a potentially more serious injury and an expected niggle, but I gues sit's how you manage your niggles (?!) I must say also there were many occasions when I just wanted some sort of reassurance that these injuries/niggles were part and parcel of my body adjusting - in the end I just told myself they were and got on with it (carefully adjusting training volumes/intensity).
Also, it kinda doesn't matter how 'fit' you are, it takes frustratingly long for your musculo-skeletal system to catch up with your cardiovascular system - especially when you've been a couch potato for 10years like me and start some serious running. I've teetered on the edge of falling into this trap , and hence why it is very true that you can't train for a marathon from the couch in 16 weeks...! My first marathon that I never thought possible is next week10 months after being a 'I hate running' sort of guy. Couldn't have done it in a shorter time frame, and wouldn't have wanted to for the exact things you highlight - injuries that go a long with increasing running volumes.
Anyway, take it easy and keep listening to your body!