Finished binding should look like the photo below. The twin-needling is at the down-folded edge of the binding next to the main fabric and the coverstitch loops cover the raw or folded edge on the reverse.
It should not look like this:
And in most cases, nor like this. Although there may be times that you want the topstitching to straddle the binding edge as a design element and in that case, it's OK!
If your stitching does not fall on the binding like in the first photo above, you need to change how the strip is folded by adjusting one or both of the two screws at the top of the binder. These guides control how much of the strip is folded into each section of the binding. Screw 1 below adjusts the top guide. Screw 2 adjusts the bottom guide.
The reverse of the industrial type binders is shown in the photo below. Your specific brand binder may look slightly different.
On a properly adjusted binder, the top fold guide (1) will protrude slightly more than the bottom guide (2). Exactly how much depends on your binder, your machine, and whether you are using an A or B style binder.
If the underside fold or raw edge of the binding is not covered by the looper stitches, loosen the right screw (when viewed from the front of the binder) and slide it a tiny bit to the right. This will pull in the guide for the lower fold and result in a binding with less underfold sticking out.
If your top stitches are straddling the binding edge (and this is not a design choice), loosen the left screw and slide it a bit to the left to make the binding top fold land a bit to the left of the underside edge.
With both of these adjustments, you may also need to adjust where the entire binder sits in relation to the needles. Once I have the binder position finalized on the bed of the machine, I mark it with a Sharpie marker so I don't need to fiddle with it again.