The majority of those orphan dots are "spot depth readings" used mostly in places where there us a deep spot or a shallow spot where the area of a depression/bulge is not large enough to bother with a full depth contour as determined by the map scale.
I've also seen them (the dots) used in a few places to indicate odd things like a "no wake area"
If you're looking at them in homeport 2.1.1, just zoom in and place your mouse over them (the dots) in the program will display exactly what they are.



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