I have one vent that overlaps a fan, and the room gets just as cool or warm as the others. It's a non-issue. The fan, if it's on, will just stir up the incoming air a bit sooner.

For maximum comfort, if it's possible, you want the vents (outlets) near the exterior (walls) and the air return close to the center/interior). But it is often drifen by what is possible, not what is ideal.

You could possibly have a problem if you run the fan in reverse. You would be pushing air against the vent.

I have seen instances (such as in one of my bedrooms) in which the airflow from the HVAC register is strong enough to make the fan wobble off-balance.

move the supplies.

best of luck.