It's not all implausible. I dated a girl for 4 years. A week before her period and during her period, she'd be reaaaaallly cranky and hate me for no reason. And then apologize profusely for her behavior later on. I broke up with her eventually, because I can't stand to be around a girl who's a complete bitch for two weeks a month.
It is possible.
Most of my point, however, is that the first thing women go to when a random man is acting odd is not, in fact "is their penis bothering them today" (even though I'm sure some men have some real problems with that), so my hope would be that he'd learn to accord this girl a bit more respect until proven incorrect.
This must've been the problem. She was thinking that your penis was bothering you.
...
what
Can't really give any help, though. If she acts like she doesn't like you, she might not like you. I'd say get to know her but most people here think friendship territory is bad.