It’s easy to go over budget or not realize all the items you need to account for until you start ripping into things and suddenly your ‘profitable’ flip is upside down.  

I run into many of the same items as an Land use Engineer.

Are some capped on certain items?  

Howdy! Noah here, new to Bigger Pockets. 
I just went under contract on a 35 unit apartment complex built in 1980 and I have to do some remodeling... YAY... Time to raise rents. 

I need all new appliances (Fridge,...

However, you can expect to recover about 50-55% of your investment when selling the home.Another good option would be to consider converting attic space, finishing a basement, or repurposing a large living area to add a bedroom without expanding the home's footprint.Some other tips to help you save on materials while still creating an appealing finished product: buy in bulk, shop at discount stores and outlets, look for overstock, discontinued items, or slightly imperfect materials, attend auctions and Estate sales, incorporate reclaimed wood, vintage fixtures, or other salvaged items for a unique look at a lower cost, build relationships with suppliers...If you have any more questions or are looking for funding please feel free to reach out to us, we're a private lender.Regards,Jackson

It's because you didn't get rid of all the food and drinks left on the studs by the electricians and plumbers, before the sheetrock crew does their thing. 

If your income isn't in a certain range or if you're not a real estate professional (amongst other items) the cost segregation might not be beneficial.

Since it's a duplex, it has one of some items (one roof?)

I own a small (72 unit) multi family in OKC and have seen vacancies go up and we have had to start increasing specials and extra items to attract quality residents to fill unit. 

You may have dodged a bullet if you really forgot to check and verify all the items.