I’m noticing that when I have several Scrivener projects open and some of them are displaying in an external monitor, when I switch to a reference manager with ctrl-y and then ctrl-y again to insert a citation, the citation is copied into a project other than the one in which I’m working.
I don’t know if this is an issue with OS, or Scrivener, or the reference manager. Any suggestions would be welcomed.
Nitram
On macOS 10.12.5 using Bookends 12.8.1, no multiple monitor, with two scrivener projects open, CMD+Y always goes to the correct project. But you must make sure you don’t focus the other project in the meantime. So I can only imagine this is some bug with multi-monitor or your reference manager (unless you also use bookends)…
I am also using Bookends! 12.8.1, with OS 10.12.3. With two Scrivener projects open on the builtin display (but with the second monitor still connected), the citation gets pasted correctly to the active project. If one of these projects is moved to the second monitor and the reference manager is invoked from the project on the builtin display, the citation is pasted to the inactive project on the second monitor. If it is the project on the second monitor that is active, the citation is pasted correctly to that project. It seems that the project on the external monitor gets priority.
And I’ve just tried switching the primary display. With the external display as primary, invoking the reference manager from a project on that display results in pasting the citation into an inactive project on the built in display. But if I invoke the reference manager from a project on the built in display (now the secondary display) it pastes correctly.
Very odd!
You have good taste in reference managers! 
It is hard to work out what is responsible: scrivener, bookends, or the OS focus code. You could try also asking Jon at the bookends forum?
I’ve been pestering Jon with another problem, which he solved very quickly, but I wanted to give him a break!
This behavior seems a result of how Spaces is configured in Mission Control. If the external monitor doesn’t have its own spaces, but acts simply as an extension of the built in display’s spaces, the call-&-return works fine. Once the external monitor has its own spaces there’s a logic to where the citation gets pasted that I haven’t yet figured out. I prefer to have the extra spaces available, so my work-around is to keep open Scrivener projects all in the same space, at least when I want to insert citations.