When I make a scenario on the map editor and test it out, enemy drop ships appear. How can I make a scenario without enemy drop ships? Thanks in advance.

Only by Lua

Or disable enemies from the activities you're using. That'll go for all skirmish missions though, so you gotta enable them to play again.

or put a layer of really hard material across the top of the map

If they appear on it, they will puncture a hole on it though. Better make it a thick layer, but you cant order troops using either method.