I expect it was probably not ill-intentioned by your agent but... are we talking about at Lease signing or at the application signing?
at City Central Realty, LLC we have specialized in rental properties throughout the Greater Boston area for over 10 years. The Massachusetts real estate laws require that at least at application before you put any money down that it be disclosed whether or not there is a fee and all of the requirements to take possession of a property.
Most realtors in this market may assume that everyone knows that there is a fee for renting an apartment. Unfortunately not every realtor is trained beyond showing apartments or they are more focused on sales and do not pay enough attention to the requirements pertaining to rentals.
They should have had you sign an Intro & Disclosure form before they took you out stating that every apartment has a fee, whether you or the landlord pays all or part of it, and that you would be responsible for this fee if you decided to rent one of the properties that they show you. They should have given you a copy of this form along with their name and RE License number printed on it. Otherwise, you have no enforceable obligation to rent the apartment from them.
We, as all realtors should, have a form that spells out what is or is not included in the rent and what move-in costs are required...
Just an fyi - legally any realtor/landlord can only collect 1st month, last month, a security deposit and a commission equal to, but not more than, one month's rent plus a key/lock change fee. It is illegal for a landlord to charge a pet fee or additional rent for a pet, a realtor to charge for their "time" if you do not rent anything, and so on. If a landlord is paying part of the fee, the realtor can only charge you the balance left over after the landlord's contribution to the fee. If the LL pays a full month to the realtor, then it is NO FEE to you. If he pays a half month, then you are responsible for the other half.