Here is the situation. I began the campaign on map #4 and the Axis started with 3 supply points and the Allies with 6. The Allies destroyed all the Italian units and used 4 supply points and moved to map #3. The Axis used no supply points. So the next turn begins on Map #3 with the Allies having 2 supply points left over from the previous map and the Axis has 3 supply points left over. The #4 map shows the Axis getting 3 supply points and the Allies 4. But the Axis controls Derna +1, Tobruk +2 and Bardia +1. Does this mean the Axis begins this turn with 3 points left over from the previous map +3 from the current map #3 plus 4 for controlling the 3 ports on map #3 for a total of 10 supply points? The Allies would have 2 from the previous map plus 4 from map #3 for a total of 7?
Yes and No. The Axis do keep their unspent supplies. Do not forget that you do not have to spend supply points to exit units from the map: Just destroying your opponent or capturing all the cities was enough. But I don't think you did this anyway.
---> BUT DO NOT ALSO FORGET that before Turn 6 only the Green supply counters are Available for the Axis (the Gray ones have not entered yet), so in fact the Maximum your can have is 6 SP (8SP for the Allies).
So the real total would be:
6 For the Italians.
6 For the Allies.
But yes, when you fall back on your own bases retreating, there is a tendency of getting more supplies than your opponent: Historically in the desert war the BIG problem was not having enough supplies, piled up at the ports, it was getting those supplies, using mainly trucks, to the front line.