i have exactly the same problem during wet weather with my pod filter. if you lift the bonnet you most likely see a few beads of water sitting in the grooves of it. Im pretty sure, at least for mine, it gets in the front grills on the bonnet and flicks up on the filter. Best bet is to barely drive it at all so it doesnt suck the water in.

Once it dries out you should be fine, but for some extra measure you can rip out your afm and give it a good spray with electrical contact cleaner