Unfortunately, I myself have found that FRP doesn't hold all that well when used for roofing applications.
I used FRP to replace a aluminum roof that the previous owner shot thousands of air nails through as they attempted and failed a rehab of that trailer. The FRP performed well for me for about 7 yrs but after that it started cracking and tearing it's self apart in places with no rhyme or reason..
It seems as if the FRP isn't suitable for extreme tempurature swings from winter time into summer time here in PA.. Typical winters we can get below zero temps for weeks at a time and in the summer, 90F in the shade for weeks at a time.. Mine doesn't have shade so summer roof temps easily can go over 120F on hot days..
For yours, the discolorations look to be rust color to me.
The rust could have come from the substrate layer via staples or other fasteners used to fasten the substrate to the roof framing.
But to get that rust to bleed through it would mean that the cracks developed over time and allowed water to slowly seep into and though the FRP layer..
I have found that FRP top layer sheds moisture well, but once the top layer erodes some the moisture can be wicked into and through the FRP and into the substrate under it that it is glued to..
Once the raw fiberglass under the top layer has been exposed to UV from sunlight, it tends to breakdown, gets brittle and flake off.
My fix to the problem was a new roofing material that can deal with the extreme expansion and contraction that happens with thin FRP (fiberglass in general has a large expansion/contraction ratio with large temp swings).. I applied a product called "Peel and Seal" (has a thin aluminum skin as a top layer to protect the rubber) over top of the existing FRP.. So far has worked well for 5 yrs for me..
I wished I had better answers for you..