We've identified the issue that allowed the mis-aligned holes in the sight arms to slip through.  This should be extremely limited, but we're doing 100% check on everything still here and contacting dealers just in case.  So far, it's 3 sets total that we've seen out in the wild, and we've got one set out of the over 1000 still here.  We're putting in an extra QC measure for this issue, so you shouldn't see any of this moving forward.  Anyone who has a sight with a twisted upright can swap them out and we'll have a new sight for you in days.  Call CS, and we'll get one on the way.  The twisted arm isn't enough to affect function on any that we've seen per se, but it's not right, and we'll make it right.

On the mounting these square on the rail, the same issue that causes the rotated upright can cause offset mounting.  However....

On sights that do not have the upright issue, it may be installation method.  These are designed with some freedom in the floating clamp to self-center, but if you force the sight forward too hard and hold it while tightening, you can force it to mount askew. This is how many mount accessories, so it's a little departure.

To mount straight:

Open clamp so it slips over top of rail.  Gently push sight forward in the slot until it contacts the front of the slot.  DO NOT CONTINUE PUSHING FORWARD.  Just slide it forward until it touches.  (Pushing forward too hard allows the floating clamp to bias back, and you can gouge the rail as well as mount the sight a little crooked.)  Now push the sight left as seen from a firing position.  (The right "leg" of the clamp is fixed, the left is floating.  Pushing left aligns the fixed leg against the rail.)  Not too hard, just to get alignment.  Now, tighten the dual-drive mounting screw. As it tightens allow the clamp to align itself.  Don't force it forward or left, just a little to keep it from wandering is all.  The sight will self align as it completes tightening. If it's tightening down crooked, back it off.  If it's not aligning properly, let the sight wiggle a little as you tighten and try it that way.  

We designed the sight to mount centered even if you just throw it on the rail and tighten it, but we may have outsmarted ourselves, since pushing it forward or forcing it hard to bias it in any direction can make it end up crooked.

Hmm, may have been a miscommunication here.  If we're pretty sure we know what's going on with a customer's product we will first send a replacement out along with a pre-paid return label for the old one.  Typically the only time we'll have someone send back an item first for inspection is if it's a new issue we haven't seen before, or if we suspect the item could be a counterfeit or some other such irregularity.
Now, with the MBUS Pro, we are working on getting back on line with additional fixtures and QC checks to prevent this issue from cropping up again.  Please reach out to us again and we'll get you squared away asap.