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I actually experienced this once in a fleet vehicle I was using. I heard the same thing as you, pushed my foot against the rubber at the bottom of the door, and all the water came pouring out. I figured it had something to do with aftermarket upfitting, considering I’ve driven numerous fleet Interceptors and have only experienced that once.
Check the drains at the door bottoms to ensure that they are not blocked so that the water drains from the door. Also, there was an issue with the 2005 Five Hundred that the bottom door seal covered the drain when the door was closed blocking the drain. Ford issued a TSB on the issue . . the fix was to trim the bottom door seal away from the drain to allow it to drain when the door was closed. I don't know how similar your PI is, but it is worth checking. If that is the case, it's a two minute fix.
2005 Five Hundred SEL
There are flaps or plugs in the drain holes at the bottom of the doors. They will get stuck because of dirt. They just have to be opened and the water will drain out. My car had this issue. It is a two minute fix