Dents in the buffer caused by it striking the detent may not be caused by the detent being in the wrong location.
Dents occur when the buffer is not depressed by the bolt carrier when the upper is closed. You should see and feel the carrier hit the buffer as you close the upper. This pushes and holds the buffer back away from the detent pin. What this means is that the problem could also be caused by the upper being slightly forward of where it should be, or the carrier being slightly too short.
None of this means that anything is out of spec. Since every part has plus and minus tolerances, any two parts which are at either extreme of tolerance levels could cause minor problems such as this, and is more common of an occurance when mixing manufacturers.
You could continue to pursue a resolution with the manufacturer since all your components are Bushy, or you could fix it yourself, depending on the depth of the dent. Dents that severly distort the edge of the buffer enough that could possibly cause the buffer to hang in the tube should be addressed by the manufacturer. Smaller dents can be quicky and easily resolved by placing a spacer on the front of the buffer, slightly thicker than the size of the dent. A piece of cardboard, rubber, or even a washer (steel, aluminum, or rubber) will work. You're only looking to add enough material to take up the space between the carrier and the buffer so that when the upper is closed, the carrier presses the buffer back into the tube, keeping from contacting the detent.
Another method is to trim the edge of the buffer using a file or dremel to notch the edge of the buffer to accomodate the detent. The notch is only as high as the detent, and slightly deeper than the dent put in the buffer. In effect, what this does is to move the face of the buffer slightly forward so that it contacts the carrier, which again keeps it away from contacting the detent.
Neither method affects the ability of the lower to handle different uppers nor do they have any impact on the function of the rifle and they are easy to reverse if ever needed (by removing the spacer or replacing the buffer).