I swapped factory disc brake setup from a Duster onto my 68 Dart. Everything turned out good however I noticed that the passenger side wheel sticks out further than the drivers side wheel. Anyone ever ran across this?

Make sure you have the correct upper and lower control arms. Check the spindles for correct application.The part numbers if stamped on parts should be one digit higher on left than right side. Even number on right odd number on left. Measure center line distance between ball joint and pivot points if no part numbers on components. If that is correct, measure distance between fender lip to frame to make sure fender is not bowed outward further on one side than the other. One of these checks should show you what's going on. This is all based that you have had a front end alignment already. Camber or tow may be off changing the appearance.

don't forget the quality of build in those days was not very good. it is not uncommon for this to be perfectly normal with one side of the car having a different amount of clearance than the other. usually, most complain about this on the rear tire clearance being up to one inch variance from side to side on the outside quarter to tire clearance. but it also happens on the front. a disc conversion can sometimes accent this if it spreads the wheel mounting surface outward. as has been said, check several key parts and compare dimensions. if nothing is damaged and the car hasn't been in an accident, likely you have a factory quality build issue/error. if so, you may or may not wish to rectify this, depending on the amount of effort required, and if it will even be beneficial to do so.

grab your tape & start comparing every relevant dimention on both sides starting at the frame rails & work outward

Look at the backspace on the wheels 1st...
You obviously went from a 4" bolt pattern to a 4 1/2"...
You had to change wheels and I think that is where I would look 1st...