I know of three places on the Bonneville that are common. The first is the gas fill area. Mine is an '03 and I think it is just starting to possibly starting to bubble just below it. I think water can get in there and it doesn't have a great way to get out. Another that may not be common to everyone, but is probably common for those of us in the snow belt is in the bottom rear corner of the rear doors. I get snow/slush that gets in the space between the bottom of the doors and the side cladding. I think the issue is once it gets really cold, that stuff freezes. Then if it gets knocked off just right, it pops the paint off. At least that'* my theory. I've got a spot on both sides down in the corner right where the metal meets the cladding where there is a spot the size of a nickle where the paint has flaked off. I tried touching in up with primer/paint in a spray can but that didn't last. The third area, not even rust, is the hood. If it wasn't primed properly at the factory, the paint starts to release from the Aluminum hood and it bubbles, looking like rust. It will then flake off once it affects a pretty large area. If yours isn't doing it yet, you may be in the clear as I think it normally starts out within the first few years.
2003 Black SLE-Stock
2000 Mercury Mountaineer
1968 Oldsmobile Cutlass Convertible-455 cubic inches of muscle