When vetting Real Estate Agents what are some big red/green flags you look out for?

Any red flags to watch out for?

This sounds like the start of a story with an ugly ending - red flags everywhere. 

Someone getting offended when being asked for proof of funds is also a red flag - you're going to buy a large ticket item... being asked for proof of funds is the norm (along with a preapproval letter if they're financing). 

When the market is red hot it's easier to be too light on rehab or push numbers too high because that's what you have to do to make your offer competitive.

Big red flag on the DIL checklist.

If a large majority of the units are owned by a one person or company it can possibly be a red flag.

There have been some great responses above so I won't focus on those points in my response, I only want to call out 1 line in your post that is a potential red flag.You say "I have recently come across a duplex in a small town"Now I don't have a problem with small towns.

What are red flags when working with an agent for house buying?

If your property cannot handle a vanilla turnover without going red, you either bought too high or dont charge enough rent, or both.