I believe the citations plugin has not yet been updated for OJS 3.0. My understanding is that this is a high priority and will be rolled in soon, it just didn’t make it in time for the initial release.
I’ve filed an issue so that we can discuss the status and how we’ll move forward in the near future.
You’ll need to make sure that you’ve enabled the References metadata under Settings > Workflow > Submission. Then you’ll need to check a submission to see that the data was ported into the metadata field of an article by looking at the submission’s Metadata tab.
Yes, Citation Markup Assistant is not in OJS 3 and currently there is no alternative – maybe there will be one later using the Open Typesetting Stack (OTS) integration, but I am not sure about that yet…