I have a 2011 Ford Fusion. My passenger side wheel sits 1 finger away from the shielding in the hub (towards the engine / forward) while the driver's side is backward. Not sure what happened to it. What could be the possible causes? I've had upper control arm replaced but everything else is OEM.
This sounds like it has been in an accident or severely hit a kerb.
You need to get a full chassis check to find which points are no longer in the correct position.
One way of approaching this at home is to drop plumb lines from each of the recognised points (usually from info in the workshop manual) and marking them on the garage floor. As you connect all the points you will, or should, find which points are not correctly located with the others.
If you don't have the info then you could start with any identifiable points such as all the front suspension location points, the hub carriers, the rear suspension points, any points on the chassis that are on both sides pressing points, holes etc