Sounds like you did not do a proper clean, strip, epoxy prime before applying your topcoat. Don't believe any of the gimmicky product hype out there, nothing replaces proper prep and product selection.

I would wash the area thoroughly, then clean with a degreaser. Then wire wheel, grind and sand blast as needed to get everything back down to bare metal. Then I would wash everything down with a phosphoric acid based rust converter prep wash, then rewash again with soap and water. Then epoxy prime everything (with a legit 2-part epoxy primer, no crap in a spray can), followed by topcoating with the topcoat of your choice. The underside I would do with undercoating, the heavier stuff you buy per gallon and apply with a schutz gun. Note, you have to apply the topcoat within the recoat window which for epoxy primer is generally 2-3 days depending on brand.