I have a Bibtex database with 1.4k entries, when I click Edit->Manage keywords and select keywords that appear in all entries I got 2.3k keywords.
What I would expect Jabref to do is to show unique keywords among all selected entries. Otherwise, AFAICT there is currently no way to actually manage your keywords.
p.s. JabRef 4.1, macOS 10.13.3