Yes - this is a BIG problem. I live in a rust belt - Toronto - we salt viciously ;-) When I bought my 2010 it had minor wheel well rust. Yes - the foam baffles for these years are there to stop road noise from going from the tires into the cabin. They also soak up a LOT of water once they are compromised. Add to that the empty channel that leaves and bugs and lawn clippings etc can fall into, and they all collect behind that vertical baffle. The combination of standing/constant water behind the metal wheel wells and also the wet/mushy organics are the issue. It rusts form the inside out - which is why bodies that have had no accidents still rust through. It is a stupidly poor design choice. Once a year (after autumn) one should take the front wheels off, remove the fender shield, then the foam baffle as well as any leaves and debris. If the foam insert is heavy with water or feels wet, it is time to replace them with uncompromised dry ones (they were surprisingly/relatively inexpensive - I forget how much but reasonable). BTW I would get a new foam set regardless as there is definitely an issue if not done previously. I ordered a new set of after market fenders off eBay - $200 USD - primed but not painted, and then a local shop rustproofed the inside fender and painted to match the body colour (white) for $500 all-in, including installation. It's not something I wanted to do when I bought it, but necessary as it rusts fast in that area and would look jimmy if I didn't. Just sanding and filling would only lead to future rust flare-ups, and you are only buying six months at a time/maybe a year. One option I will be exploring is stuffing large-hole foam filter material you can get from pond supply stores or aquariums - they use them to put over pond filters to filter debris so the pump is not damaged. The holes are big enough to allow water pass through but also large enough to stop leaves and bugs etc while allowing fresh air through. Maybe I'll post a note during good weather on youtube to show you ;-)
EDIT: as for trimming or cutting - DO NOT. There is a fine/thin seal over the entire foam, that once compromised lets water soak into it just like a dish sponge. You are asking for trouble - believe me I researched this for weeks ;-)