I'm having a similar issue:
(1) it resorts back to the original unnamed tags until you resort the tags column in finder
(2) when adding a new tag to files or folders with multiple different tags all tags are selected for all files
Here are three folders, two with distinct tags, one without. When I try to add a new third tag to all El Capitan adds all the tags to all folders. Yosemite did not have this issue.