Got into a place today that had the combustion air supply cut as an opening into the floor with a register cover and it was pulling air from the crawl. My first reaction was “That’s wrong”. It’s the first time that I have seen it done that way. The PVC exhaust vent on the roof also has an inordinate amount of moisture coming out of it. There was enough to freeze coming out. Also, this home has a lot of black marks around registers, under furniture and doors. The wife is a smoker, although not particularly heavy, and burns a number of candles. The filter on the system was not a disposable, but rather the cleanable and reusable type, and it was not dirty. My question I guess is could the combustion air being pulled from the crawl be causing some of this, or maybe the filter is just not up to the job of cleaning the air in this home? The furnace is about a year old installation and otherwise appeared to be serviceable.
Combustion air for the furnace is allowed in my area to be taken from the crawl space as along as the furnace is located within a closed closet with door. As a retired Hvac person I never did install in this manner not my choice but is allowed. Recommend you check your local codes. As for the the combustion air from the crawl space interfacing with the return side of the furnace it should not be happening. Where in the home is the furnace located.
As a guide look at “Code Check - HVAC”
Beyond that, or if something rubs you the wrong way, call for further evaluation by an HVAC specialist … CYA (cover your assets) … 
That was my thought. Unit was located in a utility closet in the center of the home. Return air was located at the wall just below the cathedral ceiling in the LR.