I love the program, and hope to use it exclusively for writing up articles in the near future. However, there are still a few issues around citations.
when selecting the citation style in the inspector, searching for the appropriate journal has become difficult - when typing the first few letters of the journal you are searching for, it offers and autocomplete-type suggestion but seems to complete it as though that was exactly what you were looking for without letter you continue to type. Try searching for "Anaesthesia" to get an idea of what I mean.
The bibliography listing for many journal styles is incorrect - in the case of Anaesthesia, the first item starts with a number "1." but the rest of the item is on a new line and this problem continues for the rest of the list. When using Papers3 with Word to make a reference list, the problem does not arise, so the problem lies with Manuscripts somewhere.
There is no clear way to edit the citation style. Many of the journal styles are out of date, or just slightly incorrect - enough to make it impossible to submit to the journal in question (again, Anaesthesia is a good example). Ideally, there would be a way to edit the journal style within Manuscripts itself - and the altered style file could be kept locally as a custom list to avoid everybody damaging the main database.
I think this software has huge promise, and if it could work a bit better you could actually justify charging more, or making it a subscription service!
Hope this feedback helps!