Smell in A/C when on could it be the filter ?

Possibly an industrial strength deodorizer was added to the vents to give you a nice impression of the service. However, in this case it may have been overkill.

1 filter. You could also try spraying deodorizer into the cabin air system intake near the hood and windshield from the exterior.

What kind of smell? Sweet like coolant or a musty, decomposing like smell? If sweet like antifreeze it could be your heater core if musty/mildewy or decomposing like smell try replacing your cabin air filter.

I don't list a cabin filter available for 2007 - 2009 Explorer.
Usually the smell is trapped water in the hvac box due to a plugged drain line. The water is supposed to drain onto the ground under the truck when the ac is on.

check ur trans fluid to make sure it is full if low add fluid -look and smell the fluid should be dark burgundy not brownish and should smell like oil not a burnt smell u did not say how many miles or if the filter has ever been changed if it smells burnt or is brownish change filter also if high mileage change also

I have had the same smell since I owned the Edge and accidently came upon an easy cure! My mechanic put a very cheap, very thin cabin filter in, instead of the very thick allergy type that was in it. Apparently the thick filter does not allow for evaporation and mold/must grows. I prefer the kind that filters pollen, etc., but will go with this very thin one from now on. Absolutely no more weird smell and it's been two months. First time since I owned the car. It definitely was my problem. Try it!

you can buy a deoderiser that kills all known airborn nasties,you spray it into the air inlet of any aircon unit,the only smell that it will NOT get rid of is cigarette smoke.that sticks to the filter/condenser and all the vents...nasty.

I'm 99% sure it doesn't have a cabin air filter. I've serviced many Jimmys and similar GM trucks of the same era and never replaced a cabin air filter or seen a reference of one in manuals. What kind of smell are you experiencing? Is it a musty moldy smell or a horrid animal smell?

Well first if you smell gasoline don't start the vehicle, check the entire fuel system locate the filter and check for leaking, also this vehicle uses a cabin filter to filter incoming air to the passenger compartment, locate this filter and replace it. there located sometimes behind the glove box door, or under the front cowling under the hood, in that space just under the wipers, If you can't find the solution and the smell persists, you need professional help ( with the car)