It is odd but it's not a problem. The paste wax your using has a solvent that keeps the wax as a paste, when you wax a naturally waxed pipe with it the solvent also softens the wax finish on the pipe and it all mixes together. It then hardens as it hazes over and than is buffed bright. The fact that some of the color came up means two things. One they got a little over zealous staining the pipe. Two that they use an alcohol dye and natural wax to finish that pipe without varnishes. The later is how you would want a nice pipe to be finished. I had a NOS GBD do the same thing years ago it'll settle down after a while.
Bearing the burden of responsibility..... It's probably my fault.
Treat your silver as if it were earthenware and your earthenware as if it were silver - Seneca, Letters of a Stoic