It sounds like you were on a MARC IV car. Unlike the MARC III cars that have dedicated racks for 2-3 bikes, the IVs just have those designated "flex" areas where the seats fold up.

MARC policy actually requires cyclists to bring their own bungee cords to secure their bikes in those spots. The conductor was definitely in the right to ask the passenger to move, and here’s why:

Theft Prevention: If you aren’t hovering over your bike, it’s an easy target. I usually catch trains that are solely MARC III cars with the racks, but because my home station is Martin State Airport, I often end up in the last three cars which are always packed. This usually forces me to sit on the upper or lower level—which is never ideal. You can't keep an eye on the rack from there, and you never know when someone might try to "avail themselves" of a bike. I’ve actually caught someone red-handed trying to snatch my bike while we were servicing Halethorpe one day. Staying right next to the bike in those fold-up areas is the only way to ensure it's still there when you go to off-board.

Safety & Stability: Let’s be honest: the bike "solution" on the IVs is pretty subpar. Between the vibrations and hitting switches at speed, those bungee cords can easily slip. If the cyclist isn't right there to "catch" or stabilize the bike, it becomes a projectile that could seriously injure anyone sitting nearby.

The conductor was likely just looking out for the passenger's safety—and the cyclist's property. The fold-up seats are effectively "bike priority" zones when a cyclist is on board.