Help Identifying components in Teensy 4 schematic
Considering the whole schematic I think


the filled dots (you encircled in blue) are nets that go to a test points
I think they correspond with the tiny round pads on the back side of the PCB, but I cannot confirm this by visual inspection only)
Typically, label these nets would have been labeled on a schematic.
the open dots (e.g the one labelled VUSB) are nets going to a connector (SMD pads or the through hole pads at the edges of the PCB)  
the 2 rectangles (you encircled in red) is a solder bridge: it is in the right upper corner: Cut to seperate VIN from VUSB. You can undo the cutting by applying a solder bridge again.