TimeQuest Invalid Path / Mis-analysis

Note that it's not considered wrong, just what Quartus does by default(along with other synthesis tools). If you look at:

http://www.alterawiki.com/wiki/register_duplication_for_timing_closure

Page 11 talks about ways to stop Quartus from removing duplicate registers. (The document is where the user is explicitly duplicating them, where in your case you didn't realize they were duplicates, or at least weren't doing it on purpose. Adding a dont_merge or disabling remove duplicate registers on that particular register might make sense.