Copying and pasting (as well as cutting and pasting) from part of a Manuscripts document into another part of the same document is, as best as I can tell, completely broken. Sometimes it just doesn't work. Sometimes it doesn't paste at the insertion point, or it changes text in a completely unrelated sentence as well as pasting.
If you copy a phrase that includes a citation, other citations may be duplicated, and the original citation is in the wrong spot. Formatting overrides (i.e. bold, italics) seem to randomly be added or removed to pasted text depending on where it was copied to and whether the source or the destination had the formatting (nb: the formatting seems to break only on new lines?).
Worst of all, half these operations can't be cleanly undone and may cause permanent damage to your document. In one case, trying to undo pasting something containing a citation actually caused my document to be filled with a giant blue blob of what looked like JSON?
Honestly it's basically completely non-functional at this point and needs a serious looking at soon. Especially considering how important and basic of a feature copying and pasting should be.