I have experienced two issues related to copy and paste functions within Manuscripts.
The first is a major delay between executing the keyboard shortcut for copy and paste and the time the text shows up. I inevitably end up pasting several copies of text before it all shows up at once.
The second is an inability to paste text copied from Word. I think the issue here is the magic citation links. When I copy the text containing the in-text citation to Pages, which doesn't support the link, and then copy from Pages to Manuscripts, I don't have the same problem, however the lag mentioned above remains.