One of the most cheap parts of the typical RV are the storage compartment seals. They can become easily damage when moving heavy items in and out of the storage compartment, so much so that the compartment may no longer be waterproof, or worse - the closing latches might not close properly.
Other than being careful, the only real options are to keep removing the dents in the aluminum frame that the compartment door seal attaches to. You can also try using common swimming pool "noodles" or water pipe insulation to prevent items from catching onto and damaging the frame.
To remove the bends, I have found that Vise-Grip pliers with a sheet-metal head is pretty effective at smoothing out the ripples in the frame. However, a 8oz ball peen hammer with a block of wood as a backing is usually required to hammer out the more significant dents.
It's just yet more evidence that RV manufacturers spare no expense at being cheap.