This happens more than people realize. Especially if others in the pen are fertile. If the hen just doesn't like him and makes breeding difficult, some won't waste their energy chasing them. My suggestion for that situation is put the rooster in a small pen by himself a couple of days. Then add one at a time the girls that are resistant. Keep them there a day or two or until they lay an egg. He should have her bred by then. Striking the mark is easier right after the hen gets off the nest. Then take that one out and put any other girl that is showing infertile in there with him.
I was almost at that point, but the two girls in particular that have been playing hard to get have been taken down in the last few weeks. This batch will tell the tale. Two hens have very obviously broken back feathers, but two have been pristine up until a few weeks ago. That's when I started cracking eggs again. He is a sibling to my other rooster, so bringing in a Redden bird is a very good alternative for me, but I really would like to see some of his chicks