One thing that I know I'm guilty of doing, and I've read that other Aspies do this too, is that I don't always respond outside of my head.
What I mean by this is when someone says something, usually you would acknowledge that you have heard, and understood this, by voicing your attention to them. This can be done by employing several different methods, such as nodding along to what they say, keeping eye contact, or even a verbal response; anything that indicates that you haven't switched off.
The problem is, while I am in fact listening, I sometimes forget to send out those cues for the other person to understand this. Sometimes I voice this to my inner voice, which is inside my head, and forget that I was not simply thinking to myself, and that the other person is still waiting for me to show that I am listening.
It's almost like having a conversation with 3 people; me, myself, and the other person; only that the other person can't see or hear the communication between me and myself. This usually leaves me having to try and save myself, in a clumsy attempt to insist that I was in fact listening...just not responding.
It's understandable that a person could get annoyed at this sort of behaviour, as I know I would, but the fact that I've become so engrossed in what a person has said could possibly also be seen as a compliment that I find the topic interesting enough to ponder. I should try harder to stop this kind of behaviour though