Schengen visa reservation of return flight from another country than accommodation

I am going for travel from Barcelona (which is my main destination) and will continue to Amsterdam. Instead of booking my return flight from Amsterdam, the travel agency booked my return flight from Barcelona.

My accommodation papers show that I was in Amsterdam 1-2 days before the return flight. After I told him that I am getting back from Amsterdam, he said it doesn’t matter there is train (which makes the story that I did go from Barcelona to Amsterdam, and then from Amsterdam back to Barcelona for my return trip).

Do they actually care about this a the embassy? Can my visa get rejected because of this?