DDR's are far from perfect, but I haven't seen any reports that this part of the DDR has a problem.
Two Things that you can try to learn more:
Make a copy of your file, remove one of these value lists from that copy and then test the layouts that were listed in your DDR to see if anything breaks.
With the DDR open in your web browser, do a text search for the name of the value list and note each place in the DDR where the value list appears. You may find a reference to your value list in a different part of the DDR that clears up the mystery. (If the value list has a generic name, you may want to temporarily rename the value list as something very unique, produce a new DDR and then text search for this more unique name.)
Thanks, Phil. I tried your second suggestion first, and while the Value Lists section of the DDR showed the value list being used on many layouts, a find on the value list name in the DDR did not show any unusual uses on those layouts; the Layouts section of the DDR showed the expected fields and expected field names. Strange…
I also tried your first suggestion, and nothing seemed to break. So, I made a copy of the value list, applied that copy to the field I needed it on, and deleted the original. A new DDR shows everything correct, but I can't help but think there's still a hidden object on those layouts…