The layer 2 scan can often show connections between devices, given a correct and sufficient response to the scan, including populated forwarding database and other information which is not reliably present in the devices.
In the case of CDP discovery, both sides of the connection need to be pointing at the other, with enough identifiable information (like interface names) in order for the connection to be shown.
In the Layer 2 device list window, the lower left pane is the connection pane. It shows information about what was seen in the scan and which side of the connection had the information, if the connection wasn't confirmed by both ends.
The InterMapper User Guide has information on interpreting the connection pane, including explanations for the display.