The Extended Family Chart picks up everone CONNECTED to a person by MARRIAGE or by BLOOD, including a child of a spouse with another spouse of a prior spouse of a spouse of your great-aunt.
I have never seen it miss such a connection.
Can you give a specific example of a connection that you think was missed so that we can retest it??
When you say "I was left with multiple islands who had not been removed - did you select the option to: "Remove ALL in this chart". If you remove all in the chart, it should removed the whole dataset you have included.
Do you understand that ALL of the islands/trees are related to each other - by marriage? The number coding relates one person as a spouse in the tree they married into. The second instance of that person is indicated in the tree in which they are shown as the son or daughter of an ancestor.
Let's say you have a mom's side and a dad's side - and you have all kinds of peripheral relatives on each side. If you detach the mom and dad from each other, or either the mom or dad from their parents - and assuming there are no other connections between the two datasets - selecting either the mom or the dad to run the Extended Family Chart will pick whichever side you want, in its entirety. If you add the number of people in the mom's side from the to the number of people in the dad's side, you should get exactly the same number that was in the index of the original file (assuming also-known-as option is the same in all three datasets.)
You can get a count, before exporting, by going to "Export all in this chart", then all of the people selected for export will flip to the right side of the screen, with a count at the bottom of the display.