Well, that confirms that the "obvious" workflow of "git pull" is dangerous. At least it explains all the spurious merges. Why on earth did it ship with this broken design? Why doesn't git pull do the right thing by default?
I believe you can flip a switch to turn on only allowing FF merges which should alleviate the situation. Certainly FF merges make a lot of things easier and "cleaner".
I guess maybe the reason git doesn't do this by default might be because the idea of rebasing early on (the "omg you're overwriting history in a RCS!!!!!") was a bit taboo and it's taken time for people to get used to the idea. Note that I'm just speculating about that, I did follow the git discussion early on and I know that people then (and still are to some degree) afraid of "rewriting history" (note that I quote that because I don't really see it that way).
Why doesn't Windows do the right thing by default?
Oh, its because a different system behaves differently.
DVCS is fundamentally more complex than VCS.