I had water in the footwells once; there was enough rain in a short time that the sewer drains backed up, I had left the car parked on the street, and the standing water seeped in under the doors of my car and all the cars near it. Are you absolutely certain something similar didn't happen? Has it visibly flooded since? Did you take out the carpet and padding and dry everything immediately, or could the water in there now be leftover from the first incident? Since we're pattern-seeking animals and can often make connections where they don't necessarily exist (like the people who used to come on here claiming an aeromod reduced engine RPM at a given speed in their non-CVT car), just want to make sure you're exhausting all options in terms of explaining this.
(I pulled out the whole interior when I discovered the water and dried it completely; no issues since and I'm careful not to park it in low spots with obvious drains).