It could be that I'm a bit sensitive and/or clueless on the issue, because I tend to be rather socially awkward myself. But the exchange about the coffee beans doesn't seem that bad to me. I mean, honestly my impression is that most of the verbal exchanges between people are empty and meaningless. Most common example being the typical, "How are you?" (and variants of), when the answer is completely irrelevant and always just a standard "good" or "fine" no matter what the truth is. Then it's like when someone has actual communication skills and interest, and communicates in a genuine, straightforward way, people wrinkle their noses.

The coworker asked a question about whether or not coffee was being made. I guess most people would have mumbled some noise like, "Mm.." without really listening or caring about what the coworker had said. But the OP actually engaged and talked about it, and formed a conclusion in response to the question. I mean heaven forbid? Now OP seems to think they don't know how to talk to people. My impression is that OP's coworker doesn't know how to talk to people, doesn't know how to handle an actual engaged conversation when they start one, if they actually had an offended reaction to the OP.

But again I also admit upfront that it could be my own "socially awkward" perceptions tinting my view on it.