Drag marks from spike shoes are fairly common. Trying to touch them up prior to applying the topcoat gets tricky for a couple of reasons, 1. typically you do not have leftover body coat material, 2. and even if you did the recoat time frames would prevent you from touching them up because now you'd have to wait for the touch-ups to cure before applying the topcoat.
For large, obvious drag marks you may be able to cheat it a little by carefully placing a few left-over flakes into the clear topcoat directly over the mark. This will help camoflauge the gouge.
While we're at it, when it comes to walking in spiked shoes remember be deliberate and pick up your feet like you are marching. If you walk like you do on the street you'll end up with these marks.