My retainer clips on the shift boot have broken and I had the dealer replace the shift boot about 6 times while it was under warranty. They have broken again and when they do I just use an plastic epoxy and glue them back on. They have broken again, but at least I can take the shift boot apart.
The reason for the breaking is that the shifter has a slight angle in it. The factory line workers did not realize this and I suspect many of the shifters were installed backwards. If you look at the shifter it should bend over to the passenger side to clear the shift boot plastic backer. I have even taken a Dremel to the plastic to enlarge it in the area where the shifter goes into reverse, first and second. That seems to be when clips break for me. If your shifter is on backwards (pointing slightly to the drivers side.) you will need ot get under the car and remove the end of the shifter from the shift rod and just spin the shift lever 180 degrees and reattach it. This will help with clips breaking in the future.