I also have a hard time when sessions go over time. I keep looking at the clock, and I have a hard time focusing on what my T is saying, and I just generally get anxious. I have gotten better at it (most of the time) since I have started trying to remind myself that my T is in charge of the sessions and it is not my responsibility to make sure they end on time.
The reason I think I get nervous is because of boundaries. People have walked all over me for most of my life, so I'm really really nervous about taking advantage of others, because I know what it is like to have it happen to you and don't EVER want to be the one doing it. So, if our sessions go over, I am worried that it is because I have made it happen, and thus I'm taking advantage of my T, and that she will hate me, etc. I know these thoughts are irrational, but I'm working on it.
Strangely enough, my T has NEVER been strict on time slots. She is often 10-20 minutes late starting because she has gone over time with previous clients, and has also gone over with me many times. When we recently started booking regular appointments again, she requested that I take the slot right before her lunch break so that we COULD go over time and not have to worry about it. (Ironically, that makes me even more freaked out because now if we go over we are cutting into her personal time, which seems even more intrusive!) So, my anxiety about imposing on her has absolutely nothing to do with anything she has done, and is all in my head. If anything she has been more than encouraging about having flexible boundaries...I'm just the freak!