Bubbling paint on door bottoms, trunk lids and fenders is an indication that the metal under the paint has corroded or rusted through. What happens is that road salts, moisture, and dirt have collected on the underside of the metal and a pinhole perforation has formed. This allows moisture to seep between the paint and the metal surface, forming a bubble. Because auto manufacturers treat steel fenders with special galvanic coatings and improved finishes (undercoat, paint, clearcoat), to protect a vehicle from corrosion, perforation is not as common on cars as it once was
The two most common spots for paint bubbles to occur are along the door edges and at the bottom of the fenders. Even though both these areas are treated with rust protection, they collect enough dirt and moisture so that over time corrosion can occur. Small amounts of rain and water from car washes seeps into the doors around the window channels. If the drain holes on the bottom of the door frame are plugged up, the water has no where to go and it eventually corrodes the metal. One of the best ways to prevent this problem is to regularly clear out the drain holes with a wire so that water can drain away.
Because of the way cars must be designed, the areas behind the front wheels and in front of the rear wheels are prone to collect moisture holding mud and debris that leads to corrosion. You can protect these areas by hitting them with a high pressure hose every time you take your vehicle to the car wash.