I am a user of Scrivener and one of the things I like to do while writing is to add side notes on why I added some text or equation etc. Such notes are not compiled in the final version of the article. I can see that such feature does not exist in Manuscripts. I hope it could be added at some point.
This is very concerning and I have encoutered such issues too on my basic version of Manuscripts App. I decided NOT to BUY the full version of Manuscript untill the issues reported by hubob above are being resolved otherwise it would be a total waste of time!
Having said that, Manuscripts seems to have huge potential.