See if they can explain the discrepancies to you so you can understand what the differences are!

If you are really concerned with the discrepancy, I would seek out a reputable local agent.

Honestly, I am just trying to get the work completed, and do so without any drama or discrepancies.

I've been asking more questions about the properties, specifically about some discrepancies with the numbers, and the broker I've been using has been somewhat hinting at the fact that nitpicking every little detail is more in the due diligence phase than the initial intro phase.  

The appraisal for this deal came back at 15% below purchase price due to a lack of suitable comps in the area, and a discrepancy on what true market rent for the space would be (despite the 10 year lease already in place.)

The problems with the UPS PO box are 1) It can only be accessed when the UPS store is open. 2) It would require intervention of the UPS staff to put it in your box, which could create discrepency if a payment comes up missing, especially if the tenant says the payment was cash.  3) It's only one location which may not be convenient to all your tennats, esp if you are talking about low income whomay use publish transportation. 4) A receipt cannot be given.We've even come up with a way to note "received with reservation" on the 7-11 receipts for those tenants our law requires us to do this for in order to maintain possession that the court has granted us.  

I asked her about the discrepency and she said that if I were to finish the basement it would be close to 1800 Sq.

One benefit to having the CPA do your taxes is that if there is an audit and discrepancies show up they can pull together all that is required without needing to scramble to do so because they will understand what is necessary.  

Although you may get over the initial hurdle, the fact that you could have the discrepancy and waived inspections, appraisal, etc., coupled with any disclaimers contained in the representation would make your claim very difficult.

Maybe there are multiple people working it and that wasn't accounted for in your est or maybe you have a more efficient way to do something and contractor agrees to lower it ...DON'T get caught up at each line item IF the total price makes sense and you've discussed potential discrepancies (if there are some).