When you see red flags, adhere to them even if the prior relationship has been good.

I've heard there's a good chance the mortgage company won't care as long as the payments continue to be made on time but I still want to protect myself just in case.

Often those lessons can't be learned, they have to be experienced.You are doing good though.

There are other areas that make good STR's that are overlooked by most in favor of the trendy areas. 

Mine is in Hueytown, which is a good area in my opinion.

Also, focus on 2 years of job/income stability.Class D Properties:Cashflow vs Appreciation: Typically, all cashflow with little, maybe even negative, relative rent & value appreciationVacancy Est: 20%+ should be used to cover nonpayment, evictions & damages.Tenant Pool: majority will have FICO scores under 560 (almost 30% probability of default), little to no good tradelines, lots of collections & chargeoffs, recent evictions.

Also, focus on 2 years of job/income stability.Class D Properties:Cashflow vs Appreciation: Typically, all cashflow with little, maybe even negative, relative rent & value appreciationVacancy Est: 20%+ should be used to cover nonpayment, evictions & damages.Tenant Pool: majority will have FICO scores under 560 (almost 30% probability of default), little to no good tradelines, lots of collections & chargeoffs, recent evictions.

I suggest focusing on properties that need cosmetic work in order to reduce overall risk, while keeping access to a good ARV.

They also normally attract really good tenants. 

If you are analyzing 100 deals, use that to take those numbers down to 25-30 days that could really be deals then go deeper with GCs to get you full details on what you would be paying on rehab and good comps.