Not sure if covered above but on most cars if water ingresses through the door (ie between inner and outer skin) there should be drain holes at bottom of door to stop the door filling up! If there is only an inner door seal the water will just flow out across the door sill probably without you knowing. But if 2 seals as sounds like here, then it may accumulate between the two until you open the door.
Normal reason for this ingress is poor seal at bottom of windows where it slides inside the door. But as with all things water leaks, it could be coming from anywhere and just travel/ find it’s own way through anywhere where there is a seal - handle, hinge, lock etc etc.
You could probably test the window seal by pouring water on outside of window and after a short wait seeing if it puddles on sill.