All Granite and Marble

I have wanted granite kitchen counter-​tops for some time. Recently I bit the bullet and decided to go a head with having them installed. I shopped a few places, but All Granite and Marble in Vestal, NY had the best price based on their website estimate tool. I rounded all my measurements up so as to get a high end price. When I went to the store, they redid the estimate and the price was a bit higher with no clear reason. Then after the formal measuring and template making (at which point I was required to give a $ 1000 deposit), I found out the price would be higher yet without no clear reason though all my options were exactly the same as the in-​store estimate. My wife and I decided to go ahead since we were not sure how the deposit refund would work, we had at this point picked out a slab of stone we loved, and the price was now in line with what it would have cost us at other places we had looked at.
Unfortunately, the counter-​top was not placed directly against the wall, leaving almost a ½″ gap between the wall and the counter top on one end. They told be the reason was because the wall was bowed out. I was suspicious about this because, A: its a fairly new house, and B: you can see where it does not sit flush against the adjacent wall, so it seemed to me the slab was placed crooked. I bought a 96″ level (surprisingly Lowes actually sells them) to confirm the wall being flat and it was. I called up the store, explaining the situation and that I was willing to buy back splash to make the gap less obvious. I was quoted a price of just over $ 300. After discussing it with my wife, we agreed to go ahead with the back splash because the gap is quite an eyesore. However when I called back the price was now increased to over $ 500. I emailed a picture of the gap, to which I did get an apology, but no change in price to rectify the situation.