could be sunroof drains , i just clean the seals regularly with car wax or you could try some silicone grease .
i have 2002 4.4i and my doors leaked depending which doors were getting wind driven rain .
water runs down windows into door and heavy rain will accumulate because the drains can`t cope and so water gets past membrane into door card . you will see when door is closed there is a gap from floor to door card so water drips from card then can`t get past door seal so soaks carpet .

i sealed cards at base then drilled 2 holes to accomodate plastic pipe from soap dispenser , the pipe closes onto frame seal and allows drainage .
also on door base there are grommets , you can puncture these to allow more drainage .