On the face of what you say it appears that the terms of the contract were not enforced. Normally it's the Listing Agent's role to make sure that the transaction moves forward per the contract (at least IMHO).
Check with a Real Estate Attorney regarding legal remedies. It is my understanding that if a contingency is not used (meaning if someone is supposed to perform an action, and does not) if the seller or their agent does not try to enforce the action, after the time frame lapses, the requirement is considered mute.
So in action that means (speaking for me) if I have a buyer that is not cooperating (they need to provide an additional deposit ten days after the opening of escrow), on Day 9 I send over a "Notice To Perform" signed by the seller, informing the buyer's agent that if the buyer does not submit the funds as agreed we will cancel the escrow.
Then if Day 10 at 5pm comes and not deposit, then we execute a cancellation of escrow. Normally if I was representing the seller I would not open escrow with less than 3% deposit at the time of offer acceptance. I would counter back stating that the buyer needs to provide a 3% deposit or it's not worth opening escrow (as you have learned) because there really is not pain for the buyer if they walk out on the transaction. It's three percent for a reason...
Yet the entire time, only amount deposited was $1,000
So what happens had the buyer not deposited anything?
You should be upset based on what you are telling me.