Not the butt or crotch area but the groin muscles, left upper inner thigh. Could be borderline hamstring.
This is really weird issue for me because I have a long background in bike racing. I no longer race but still ride a lot, do some hard group rides and play ice hockey 2-3 times a week.
I'm fit in general. I do LOADS of various leg exercises so my groin is solid for hockey. I still ride lots in the summer so my legs are still strong and I'm used to the miles. But as soon as I try to ride longer than 30 minutes on my bike in a trainer, my left groin muscles start to really bunch up.
I don't think this is a bike fit issue, this is the bike I use on the road. It's not a seat issue. Yes, there is a thick book underneath my front wheel. I stretch a decent bit so I don't think this is a flexibility issue, but maybe.
It's such an odd issue to have and I've had it for the past few years. I always assumed it was from bearing down on the seat in a weird way but I don't really feel uncomfortable. (Although all cyclists have a loose relationship with the concept of comfort.) Certainly doesn't feel different than riding on the road.
I'm just at the point where I want to try to sort it out so I can put in some solid basement miles this winter.