A stone chip for sure would have initiated such rust to occur. Plus rust will build up first along edges and creases, not to mention Honda's do rust more than other cars so I would suggest rustproofing each year before winter.
04 with 200k on it, no boby rust, just rail dust but that can be remove by clay barring my car, only rust spots are just the two or three on my hood from stone chips, donno how your 06 is rusting already, do you part your car in a garage or indoors over the winters?, if so it could explan why your car is starting to rust already, cause when you park indoors in the winter, any salt that on your car with start to travel into all the seems (ie. the seem between the back bumper and the fender) from the snow melting, i try to only wash my car about once a month during the winter as to keep the snow and salt frozen onto my car, helps prevents rusting, but we do live in canada and no matter what you do or how hard to try, the salt is just gonna eat your car lol
why does your bumper fit like shit and your getting rust cause your bumper is rubbing out the paint and the water is just sitting on unprotected sheet metal, was your car hit or something? see if you can get your bumper to fit better and buy some touch up paint and just fill in the area where the paint is gone, it doesnt have to be perfect cause your not gonna see it.
take off the front bumper and look and see if anything is bent, if not try to put the bumper as far forward as possible when your re-installing it, also check your fender gaps make sure they are good and even and not pushed forward too, try that and see how it fits, then buy touch up paint and fill in the rusted areas and just keep a eye on it, or take it to a body shop and asked them what they would do and do the work yourself, i do that all the time lol