It is quite possible, but very rare for the netlist to get confused. If the circuit simply don’t seem to add up correctly, check that all nets connected together have the same name after running the netlist on its own (blue "N" button). Mousing over each wire will show its net name in the Main Window status bar. The offending nets may need to be redrawn. Reset and renumber all net names by the Edit menu, or the brown toolbar buttons ("rn", renumber). Clean up the reference designators by automatically renumbering them via the Edit menu, or the brown ("rd", renumber designators) toolbar buttons.
Lower Level Schematics
In flat netlisting mode (default) lower level schematics usually have to be closed for the netlist to function correctly if more then one same schematic block is placed. Closing the file may also be required to clean and/or update all parameters It is also a good idea to use the auto renumber wires and reference designators from time to time.
Modified wire names:
If wires are moved after a simulation is run, in most cases its will erase its node/net name. This means that you will not be able to probe that wire with a test point or alt-click. It may be a good idea to always view component properties by mousing over the symbol and pressing the "q" keyboard button rather then by double-clicking on it. A double click might also inadvertently move the wires attached to the symbol.
Other simulators often lock out the schematic to avoid this issue. This approach was not taken in SuperSpice as this technique can also have undesired results.