There is a facility in X-Plane to fix problems with navaids, but like most things in X-Plane 10 the user interface is not exactly user friendly.
Location --> Local Map
Check the "Edit" checkbox in the top right of the screen
Select the offending ILS (remember the localiser is located at the far end of the runway as you approach to land) and use the controls in the bottom left of the screen to nudge the position and/or the direction of the localiser.
It helps if you respawn the aircraft on the runway concerned, as X-Plane will then place the aircraft exactly on the centreline of the runway. Then you can zoom in and nudge the controls to bring the localiser centre line into alignment with the aircraft silhouette.
IIRC, you don't need to hit any button to confirm - the changes are live immediately in the simulator as soon as you exit the local map screen. However, X-Plane will ask whether or not you want to save the updated data when you exit the sim - so you can feel free to experiment with this, and you can always abandon your edits if you make a complete hash of it.
Also please be aware a few airports have offset localisers - please check the approach chart before editing! LOWI is a good example, the initial approach from the east tracks the localiser on 255 degrees, but the runway itself is at 258 degrees. Whilst it is easy to fix the alignment of a normal localiser using the actual runway as your reference, an offset localiser is more difficult to fix (and more difficult to see any problem in the first place).
Here is a video of someone editing the LOWI localiser (although he actually calls it the glideslope, which doesn't exactly instil confidence). I am fairy sure he is doing something badly wrong here, which is why I put the video at the end of my post. The charts I have for LOWI say you should track this localiser inbound at 255 degrees, but here it seems the localiser is set to 256.89 degrees in X-Plane. However, rather than adjusting the localiser heading to 255 (which may not be correct but would at least have had some logic to it), he instead moves the position of the localiser south until the centre line crosses the centre of the threshold of RWY26. Sorted!
Anyway, with that disclaimer out of the way, here's the video... at least it does demonstrate how easy it is to edit navaids...