I've had this happen once. Went to check for eggs in the morning and noticed on of our boys in the nest box. I didn't think anything of it at the time.
Went back out to check for eggs a couple hours later and found that the second rooster basically was putting him in his place so he was cowering. We seperated him from the rest of the flock right then and there.
If you don't have a second rooster, then I'm not sure. I'm sure other members will come along and post their experiences.
Cowering was my only thought, but there's nothing for him to really cower from other than the neighborhood cats who seem to have taken a liking to my yard. And none of the other birds seemed to be worried about anything.
I have a 16 week silkie roo that has just started to jump my 7 mth hen. He follows her everywhere and jumps into the nest box as well. Sometimes she kicks him out though. I thought he was wondering what she was doing but it has been happening like this for days now. She lays an egg and will not sit on it the roo hangs aroung the egg for a while then losers interest. Chickens are definitely a strange breed lol