If you have an active root...over time it will grow back in there unless you excavate, cut and remove. 

Purchase price: $105,000 Cash invested: $90,000 Property needed some serious rehab, from trees roots destroying the basement walls, to plumbing, electrical, to roofing, landscape.

So can I calculate my cash on cash return like below $40K(appreciation)/($42k(Down payment)+(2.1K(Monthly payment for Mortgage+HOA)*36)) = 40/(42+75.6)= 34% so the annual cash on cash return is about 1.34 to find the cubit root.

Do you think this issue is specific to banking services or what do you think is the root cause?

That is crazy that there are not more 2-4 family in a market like Midland-Odessa with a ton of transient oil field workers that do not always put down roots.

So I have never gotten to the root of what people dislike about it.

Can anyone recommend good companies to root cause  and implement solution to fix this issue?

I would say on a rental property that's unrealistic, if it really is an issue on a property, better to address the root cause.

I guess I can't wrap my head around the fact that anyone can make an argument as to how the doors and windows being left open was not the root cause of this issue.

Generally no because the root system is still in place.