@Agustin Conti  your problem is not the size of the late fee, it is "Because In the past I have not applied the late fee," Some people are like this. 

There's a lot of factors that influence owner occupancy purchases beyond simply the economics so its difficult to say there is a right decision.

This brokerage only charges $495 in transaction fees plus $30 broker fee… that’s it.

Going to jail over charging late fees seems excessive... 

You could potentially do this, but they may want to charge you a much higher flat fee rate than you would otherwise pay with a percentage.Also it depends on how the listing is set up. 

You must pay management fees, maintenance, taxes, insurance, and other expenses, such as vacancies.

Quote from @Josh Cocker: Hi All, I've got my first purchase here in US under contract & just a quick question as I'd love to hear some answers from seasoned investors / lenders etc  (I am originally from UK and my experience with mortgage products and fees is very different to what i am learning here).I am purchasing a Duplex which will be my primary residence, and looking to borrow around $200,000 - typically what will be the additional fees / cost i should expect of this loan (presuming no point buy down etc).Thanks in advance, and apologies for asking such a basic question. 

Quote from @Lauren Kormylo: I would list it separately as a "Community Guest Fee", not just as a management fee.  

I am going to try using a flat fee MLS service for the next flip as realtor commission is very high in my area.

We consider the fee an Admin fee.