I like sleepy sex…I think?

Last night, me and my bf went to a Halloween party. He drank but I didn’t because I just don’t really like to. I’ve been dealing with a stomach bug for the past few days and I started feeling really sick so we left at around midnight (we got there at like 10ish). Anyways, we had talked about having sex earlier that night but I didn’t really think we were going to anymore because I wasn’t feeling super well. Maybe like an hour or so after we got home, my bf started to initiate sex. I was like half asleep but didn’t really mind it honestly. I was still feeling a bit sick but I wanted to. It started to hurt after he put it in so I asked to stop and he got really worried that he had taken advantage of me or something. I usually am pretty open to having sex after waking me up and have even asked him to do it before. This time he got really anxious because I did start to freak out after it started to hurt (sometimes it gets kind of tight and feels painful to have sex). I told him it was okay because I didn’t mind it, it just hurt, but he’s nervous that I’m only trying to make him feel better. I think it’s just a matter of miscommunication but now it’s making me more anxious that it’s something bigger. I enjoyed it and have enjoyed it before in the past but something just felt different about last night I suppose. Is this something people deal with their partners or dealt with before in some way? And if so, how can I go about it so both of us are completely comfortable with it?