The best laid plans always look great until 2 or 3 unplanned and unexpected things happen at the same time. 

I don't know about the location where you live, but I would have to disclose a "noisy neighbor" situation in California.When I sold my personal residence there in 2015, the PRDS (Peninsula Regional Data Service) Supplemental Seller's Checklist form from my realtor asked about items such as (to highlight a few of the 25 categories): animals (squirrels, crows, flying and crawling insects), neighborhood conditions (vehicular traffic noise on the street, aircraft noise from the local airport), and governmental issues (nearby street undergoing a beautification upgrade).Californians might sue each other over the silliest of things, but the lawsuits are real and suck up valuable resources when they happen.

That looks like a squirrel hole, so you probably need to trap the squirrels first before fixing that soffit.I used KO Roofing in Delaware County to replace one of my properties' flat roof and they were reasonably priced and responsive.Good luck

And right now being first of September already, you're a squirrel that just realized you have no food for winter.

The Exotic  Animals section was pretty funny: Tarantulas  Ferrets Skunks Raccoons Squirrels

In general, insurance provides coverage for many, sudden, unforeseen and unplanned events.

Now that he is almost complete with the project, he is presenting me with another unplanned expense.How do you deal with contractors that introduce new fees during the project?

A lot of it comes down to the math and the numbers, if you have arrived at  certain guidelines of deals you will accept, then search until you find deals that fall within those parameters (make sure that you won't have a lot of unplanned additional rehab or fixes after you purchase, that was my big mistake on one of my first ones), and then if the deal hits those numbers, pull the trigger!  

My biggest lesson was a $7000 unplanned expense when I learned that the entire sewer system under the house was filled with roots so thick that I had to pay for complete replacement from underneath the house to the street. 

I am responsible for rodents like mice or squirrels in the attic.