If they have an legally binding agreement, you need to honor that agreement and pay the fee.If you failed to mention to the agent that they are going to get paid, and then explained how, of course they won't present the offer.

Curious if this is normal practice or in other management agreements people have signed? 

I wouldn't have brought a plumber out for a smell like this without tenant's agreement to pay if nothing was wrong. 

You've only owned it six months, so you probably haven't dealt with vacancies, maintenance, or capex, but you should be setting money aside for those things.Your partnership agreement (if you have one) should address exit options.

Review their management agreement.

We signed P&S agreements on 6 different properties totaling 20 units approximately 8 months ago and received a call today that the price we thought we were buying at has to-be increased on average 13% due to the increased cost of construction.

Review the agreement for how the UPREIT will work very carefully. 

We started with an offer of $1,000, but after some back-and-forth, we reached an agreement at $1,500.

Is there that kind of flexibility in a purchase agreement?

Investor pays $2K program fee and 25% of the note acquisition price (they finance the remaining 75% via a participation agreement - at 12%).