ForceDirectedLayout doesn't seem to do the job as intended

Hello to everyone.
I’ve started to learn your library several days ago to discover if it’s able to meet my project needs.
Everything was great - Nodes&Links formatting, layouts, high flexibility. Detailed API documentation helped me a lot. But after I’ve tried to load to my diagram a bigger amount of data (~5000 rows representing links between entities) diagram didn’t appear to look not as I’ve intended:
1. Layout looks messy overall
2. More than a half of the links aren’t connected. Which is incorrect due to the data model.
I’ve already tried to tweak maxIterations property value.
maxIterations: 1000


maxIterations: 1500

So, what is the question:
How do i make the diagram look more like https://gojs.net/latest/samples/incrementalTree.html , but in bigger scale with no separate nodes?

let diagram = (go.Diagram, me.domNode.id, { initialContentAlignment: go.Spot.Center, layout: (go.ForceDirectedLayout, {maxIterations: 1500})
});

Let’s first make sure your graph is what you expect it to be. Could you please show the node data of one of those “not connected” nodes and the link data for all of the links connecting with that node?