Aha!
I think I found the issue...
If I enter "Foo & Bar, Foobar" in the field directly in the custom metadata it works just fine and returns the tags:
Foo & Bar
Foobar
Things turn weird in the tag editor...
If I add the tag "Foo & Bar, Foobar" and hit enter, I get 3 tags:
Foo
Bar
Foobar
If I add the same tag "Foo & Bar, Foobar" and hit the plus sign I get 2 tags:
Foo
Bar, Foobar