To me, simple handling of references is, so far, the only real benefit of using Manuscripts.
Editing the text sometimes cause strange behaviour, as others have reported. One example: I changed a whole paragraph to italics, to mark it for further editing, whereupon the cursor jumped to the succeeding paragraph and couldn't be moved back. Stepping the cursor, using arrow keys, resulted in the cursor jumping past the italicised paragraph as if it didn't exist.
But, I can accept some of the erratic behaviour, IF the app can handle references exceedingly well. Dynamic updating of the reference list is one such thing, ability to manually enter references in the text which then automatically are included in the reference list is another. Other requirements: An easy way of changing the way references are presented both in the text and in the reference list for all references according to the requirements of the journal, including those entered manually (see above); an option to have the author(s) inside or outside the parenthesis; the reference list warning if required data (volume, page number, etc) is missing; ...
If I have to do a lot of manual editing of the references, re-entering incomplete references to to update them, etc., I will stick to Scrivener for my writing and export the finished text as rtf and fix the reference list afterwards, because Scrivener is by far totally superior as writing software.