My company does have a $299 transaction fee for either buyer agreement or seller listing agreement, in addition to and regardless of the commission structure. It's basically an admin fee used to offset costs of signs & placement/removal, printing/scanning, driving, gas, office space, etc. We can choose to have our client (buyer or seller) pay this fee at closing or we (agent) can pay it from our commission if we want to give the client a "break" on fees. If I'm getting a healthy commission from a seller client, I probably won't charge the $299, I'll either eat it or deduct it from the cooperating broker's fee. I just make sure everyone knows there is this admin fee and who will be paying it.
My thought on this situation is if you paid an earnest money deposit you should get that back from the title company. Write down your costs associated with this learning experience and decide if it's worth it to retain an attorney ($5,000+) and pay their hourly fee ($150+) to go after someone who seems like a deadbeat anyway. Are you expecting a court to force the sale to go through? Do you want to be paid back the money you are out? You need to figure out what remedy you want. Getting a judgment from a court does not mean you get paid anything from the deadbeat. Maybe you can get a lien on the property so that if and when it does sell in the future you can get your money back as any liens will come up in the title search.
I can imagine how excited and hopeful you were to become an investor and even get to live in the unit too. Next time the inspection or appraisal comes back wrong don't be afraid to back out of the deal. I'm not sure about your state but in Florida as the buyer you have that right, during either the inspection period or financing/appraisal period. It seems like there were plenty of red flags and you should have been asking these questions long before getting to the closing table. Unfortunately, this is an expensive learning experience, but you did learn something. Do not make offers until you get all the paperwork you need to make sure the investment is sound and you can verify what the seller and his agent are telling you. A building you think is a 3-unit suddenly becomes a 2-unit - you're already losing money on this deal. If they were not cooperating on providing documents and records, etc., then you should never have made an offer - you should learn to listen to your women's intuition. Also, not sure why your agent didn't advise you better. IMO.