Grease spots, I suspect, Plebs. Front doors anywhere near a road can easily pick up oil and grease from exhaust fumes.
I guess the door was already primed, but any bare metal should have a metal or universal primer applied first. It's a bit more of a problem now, since you have a finish coat already applied.
What is worth a shot, is to...
Really sand down the affected areas, taking the new top coat with it.
Cover these areas with a good stain/grease blocker.
(Zinsser "BIN"; or Ronseal "Stain Block"; there are others.)
Undercoat over the Stain Block, then top coat.
Same thing applies whether it's an aluminium or a steel door.
Note to Ginge: most volume builders use steel doors these days. So much more stable than timber. fewer call-backs. Just don't try to "shoot" a door in by planing it ;o(