Hi, I've been having some water ingress lately and I assumed to be the driver door that is a little misaligned, the car started to smell a little like mildew and so did the carpet, so I switched back to rubber mat, but today to my surprise I found out It wasn't comming from the door seals or drains, but from under the footwell itself, could this be a blocked scuttle drain ? 

Check the bulkhead under the plastic grill and also whether the water is appearing under the car when you poor water onto the roof drain.