What do you do when your own notes contradict the evidence?

I've spent the last couple of days re-reading a transcript and my own notes from a case I lost, and there's a gap I can't close — the record says one thing, my memory insists on another. Do you keep trusting the paper trail, or do you follow the gut that says something was missed? I'd like to know how other people hold that kind of doubt without it eating the work.