I am having trouble figuring out what is wrong with these nets? "Design -> Netlist -> Clear all nets" will delete only the functional ones and these unconnected ones remain. Can anyone tell me what happened and how to fix this? Thank you.
As these traces are not assigned to any net, they are not deleted by "Design -> Netlist -> Clear all nets". There are two possibilities to do so:
Use "Route » Un-Route » All", which clears all physical connections on your PCB (https://www.altium.com/documentation/17.0/display/ADES/PCB_Cmd-UnRoute((UnRoute))_AD)
Right click a trace -> find similar objects and select the layer and switch to "Same". This selects all tracks on the specified layer and you can easily delete them