VC not in network, but still has overlapping VCs

Hi, thank you for the software.

I my analysis, i have many nodes labelled as 'Overlap (VC_1/VC_2)', but VC_1 is entirely absent from the network and 'genome_by_genome_overview.csv'. Moreover, these nodes are highly (visually) clustered with VC_0 but not VC_2 (which is visually far away and has no edges to the 'Overlap (VC_1/VC_2)' cluster).

Any suggestions?