Chains rub the front derailleur for 2 reasons:
1) The limit screw is preventing the derailleur cage from moving as far as it should.
2) Normal rub caused by the chain's movement from shifting the rear. Solution is to "trim" or "microshift" the front just enough to stop the rubbing while riding.
Perhaps you adjusted the limit screw too much, when you actually just need to trim while riding (#2).