Nob NTB fraud? Plano Texas

My daughter came home saying her flat tire light was on in her car (with less than 10K miles and when it hadn't been driven all summer.. she only got back in town 2 days ago).  We BOTH went out an saw a nail in the rear passenger tire and it was hissing and releasing air. It was located in the MIDDLE of the tire.  We brought it to the NTB tire store (less than 1 mile from our house) and they asked to leave it there for 2 hours because they were backed up with other customers.  They called me 2 hours later saying that there was a hole in the side wall and the tire could not be repaired.  I asked them about the nail in the middle of the tread. The manager said there was no nail there and the hole was in the side wall.  My daughter and I went back to the store and we all looked at the tire. There was no nail but there was an obvious spot in the middle of the tire where the nail was.  Even the manager saw it.  In addition, there "miraculously" was a second hole in the side wall.  They manager said they did not see the middle tread hole and that wasn't what they noticed was leaking... it was the side wall hole.  We both told him the store was less than a mile away from our house.  He said that nails fall out of tires very frequently and it was common for that to happen so by the time we get to the store, nails that we saw may not be there.  In 30 years of driving with between 15-20 flat tires.  I have never seen this happen.  I don't know how we could have gotten TWO flat tires in the same tire in the span of less than 1 mile.  I don't know how a nail that was lodged 100% into the middle of the tread mysteriously disappeared by the time we drove less than a mile.  I am very disappointed with this store.  Maybe I am wrong, but to me this is really really suspicious.  Did their mechanic/technician put an additional hole in our tire?  How often does a tire with less than 10K miles get TWO holes with no nails when less than a mile earlier TWO witnesses saw a nail in the middle of the tread?