Not the first thing you think about but check it next time you do the air filter, it might be in bad shape if your bike is a few years old.
The issue
The door seal is made of a soft foam that doesn't age well. It could be allowing water to get in when going through water crossings for example.
When you clean the air filter it's nice to also thoroughly clean the inside of the airbox and the door. I tried to remove the seal strip of the door but then realized the foam was breaking in pieces and was completely flat as shown in the picture above.
If you never take it off the groove, you might not notice it but might be compromised and could allow water to get in.
The solution
Make a new seal with a better material!
Instead of using this type of not so durable foam for sealing material, you can cut a new strip into a more rubbery type of material like automotive weather stripping or any other soft rubber material than you may find.
Remove the door and take the foam strip of the groove
Check if still elastic and holding together, if not, it needs replacing
Cut a strip about 4mm wide your new sealing material
Install the new seal in the groove
Screw the door back on
The picture below shows an example of a really nice rubber compound still soft enough to compress well but way more durable. Here I use only the flat portion of it.
Bonus is the tape in the back allowing to glue it in the groove.
NOTE: Applying your new seal with a fine flat blade screwdriver helps a lot.
You can also pull lightly on the strip to make thinner as you push it in. This will make it easier.
Also when you are about to close the loop, cut a little longer and compressed the end in. If you don't, it could retract/move over time leaving you with a gap and thus no seal.
You are now better prepared to ford the deepest rivers with the assurance the water will only get in from the top!
Or if you use a high-pressure jet to clean the bike, water will not get by the door and in the airbox.