I can only guess at what car you are talking about ?, but on some the motor is directly below the pollen filter/air intake, and water can drip down and short the motor, usually ok if motor taken off and dried out though.
It is normally I have found the base of the pollen filter assembly that leaks, I take these off and seal with loctite 5900 or 5910, then screw back down end of leaks, on others I beleive there is a bit of the upper part that secured to the firewall/bulkhead that breaks leaks.
tabetha