I have also had this happen when quilting with minkee on a LA. In my case the Minkee was white and the top fabric was a deep rich royal blue. I conferred with other longarmers and the general consensus is sometimes it happens and is considered a general risk when using Minkee as no one has come up with the one common denominator when it does happen. Some think it happens more often when using a cotton thread as opposed to a poly thread. Poly is more slippery and cotton more grabby so the theory is the cotton thread is pulling the minkee fibers through the quilt sandwich with each stitch. I don't believe it goes away with time, use and washing. When it happened to me, I immediately contacted the quilt's owner and we opted for a different backing. I was using cotton thread and W&N batting. I picked out what quilting I had done and reloaded the quilt with the cotton backing and all was well. This was a high pile minkee, the kind embossed with a pattern.
I have not used minkee since that but I am willing to give it a go again as I have two pieces in my stash destined to be backs. Both are lower pile minkee. So we shall see. If it does it to me again I will swear off minkee as a backing and stick to cotton or flannel.