Not saying you can't patch it. I carry Eternabond in case I do something to rip my roof. If my dealer did it or in my situation a tow company, I would want a new roof. In this case they haven't purchased it yet. I would at least want a discount if the roof was in otherwise good shape.
One other thought if the dealer didn't do it, water travels under the roof membrane. the theory is that the backing of the membrane wicks the water to different locations. Check the entire inside of the trailer for water damage. Rub your hand on the wall and push firmly on every wall surface particularly in cabinets and other places that you don't normally see. If it wasn't the dealer you don't know how long its been there. If it was the dealer and you are otherwise happy with the trailer I would get some money off for the damage.