Originally Posted by
Non-NonRev
The OP asked if booking through a travel agent would have prevented the difficulty. Maybe - if the agent was a certified specialist in travel to Europe and who was conversant with Schengen rules.
The other mystery is why single entry was chosen - to save money? Poor choice if true.
It's the Schengen visa-issuing authority that ultimately decides if the visa to be issued is to be a single entry visa or not.