Extra nodes with different layouts

When I go through the tutorial using the tutorial datasets and files, I try to change the layout to other formats with y-files (for example organic) it shows a lot of extra nodes. I cannot find a way to remove these extra nodes that don't appear to be linked in the network. Is there a way to remove these from showing? I have Cytoscape 3.8.0, the current version of CyTargetLinker, and MacOS Catalina 10.15.4. Thanks!

[mkutmon]

There are a couple of weird things happening since the latest Cytoscape update. I still need to figure out why they happen :(. Thanks for reporting this one. I'll try to fix them asap.
The nodes that you see should be hidden (so not visible but still there). For now, you could select all nodes in the connected network and go to File -> New Network -> From Selected Nodes, All Edges. That will create a new network with only those nodes.