Hi Mihaela, there are several types of co-citation analysis in bibliometrix, the author co-citation network is created using the first author in each reference. There is a small example in this video Co-citation analysis with bibliometrix - YouTube
I'm not sure how you merged both datasets, there is an option in bibliometrix with mergeDbSources but it does not merge the reference variable. I merged them with tosr package (it is not perfect but it is useful)
Hope it helps you.