Simply put.

Simply put, does anyone have suggestions of how to dispute this with the city?

There are going to be three levels of addressing this 1) things you can simply go there and do anytime (pick up pet waste and throw it away) 2) things you can do given proper notice (enter the unit and inspect, repair damage etc) and 3) things you can only do given proper process/procedure (notice to vacate, increase rent etc.)

I don’t see how he could simply independently come up with such a high price without discussing it with me first. 

They likely do not have access to those easier sources of capital though because of their shady business history and practices.Good investors do not need your money or partnership. same s**t to syndicator as well, if they do lot of marketing, run away ..... chase syndicator that doesn't need new investor lol

I just don;t see the demand.

So that’s what I was simply saying was a moot point on the front end discussing with a seller.

Just because the information is not as readily available online doesn't mean there aren´t people (agents, builders, notaries, accountants etc)  and resources that can prove to be invaluable. 

I'm assuming it works by using this non-refundable EMD or they are simply daisy chaining.Ultimately, how can end buyers be most protected from fault of the wholesaler or property owner? 

Out of state seems harder to break into simply because I'm not there - maybe Hoboken /Jersey city or further like @Eric Hajdu mentioned are better places to start.Out of state is not difficult to get into.