There's a certain healthy level of minor flirtation to be had in all normal human interaction (even just a tad towards people of the same gender, even as a heterosexual) that's socially acceptable, even when in a relationship. Chances are, for her to be seriously upset, you were likely going beyond flirting and into the realm of obvious sexual innuendo.
Then again, for nearly every male, as it seems, obvious sexual innuendo is what they consider "flirting." Most men have no flurking clue how to interact with women outside of trying to get in their pants, to be honest. There's a natural social flow that a lot of men just don't understand. And yes, that started out as a typo a couple sentences ago, but I went with it. I kinda liked it. XD
Anyway, reading your OP, you don't seem like a terribly pleasant person anyway. Using her for support?