It was a recent-ish TV programme - from my addled memory:
Bader claimed when he was released / in memoirs etc he was downed in a MAC with a LW plane but when he landed was entertained by the local Luftwaffe squadron he said he'd been shot down.
Luftwaffe records claimed no kills in that sector that day. One of his squadron claimed a 109 but none were lost that day. The conclusion was that one of his squadron had downed him in error as from certain angles in the heat of battle the new mark of Spit (not sure which) looked like a 109.
They concluded Bader was either confused or (more likely) knew what had happened and covered up a blue-on-blue for his, the other pilot's and the service's reputation.
These sources relate to that TV show
Friendly fire - Wikipedia, the free encyclopedia (see 1941)
Who Downed Douglas Bader? - Digital Spy Forums
These and my memory are not conclusive proof but do illustrate that combat is very confusing and blue-on-blue is very probable. This incident was investigated due to the pilot's fame so one can only imagine how many others there were that haven't warranted investigation.
I think another point to consider is that these incidents still happen nowadays with IFF, GPS, much better comms etc etc. With all these limiting factors not in place it must have happened a lot more in WW2.