Obtaining and possessing the proper documents for your travel (passports/visas) is entirely your responsibility and not the airline's or travel agency's. As long as an itinerary is a valid routing for a particular fare the airline or agency can sell it to you. When you book online they don't ask for your nationality and what passport(s), residencies, visas etc. you hold and then only display itineraries that are valid for your particular situation. Again it's up to you to determine where you can transit without a visa and when you must obtain one to do so.
Expedia should be able to change your itinerary so that you only have one stop in Europe and can transit without obtaining a visa. They will, however, charge a fee to do this as well as adjust the fare and charge you the difference. Sorry but unless you can get the necessary visa changing the ticket and paying the fees/additional fare is the only way to go.
I'm sorry to hear you are having difficulties with the Italian Consulate but that has nothing to do with the airline or the travel agency. Have you tried going to the Consulate in person? If you bring a print out of your e-ticket confirmation and itinerary you might make better progress face to face.
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