O.K. what we are looking at here is a muffler that is set up to use the stock Rocket L/H muffler mounting bracket.
If you were to rotate the unit so that the inlet tube was horizontal so as to align with the horizontal cross over pipe, the mounting points would be rotated around to suit the stock mounting bracket.
But then the tapered end piece would be out of whack.
As you have said this L/H bracket was not with the bike when you bought it so you needed to purchase this separately.
Again as you say there is a R/H mounting bracket supplied, this makes sence as the stock R/H bracket is set up to support the two stock mufflers on the R/H side.
So the problem is that the orientation of the rear section of the muffler, the tapered piece, is off.
This where this the main body of the muffler has not been orientated correctly in the jig when the inlet tube and the mounting points have been attached.
So yes, it has been assembled wrong.