I've actually had this experience, multiple times, on GWR IETs. GWR does allocate bike spaces on IETs, and technically you can't travel on one without. However where this becomes a problem is either when people travel without a reservation or put luggage in the bike areas, despite the lights above showing they were booked. I came across this situation on a train from Didcot to Bath last year, and with no other spaces I tried to stand in the corridor next to the bike locker, leaving enough space for someone to get by. Unfortunately the Train Manager came along and informed me that he couldn't allow a bike there, an promptly booted me off the train at Swindon.
This was despite showing him the paper ticket showing him I had a reservation for this service, in this carriage. He informed me policy is that they can't ask anyone to move luggage or bike out of the area once it's been put there, regardless of a reservation, and therefore I'd have to be the one to get off. It seemed a pretty widespread policy, as I was booted off the following IET at Chippenham, despite explaining to the manager I had been booted off the last one with a reservation.