To those have made repeat measurements and have found different values - you are experiencing the life of a scientist. All measurements are subject to random and systematic errors. Just repeat the experiment several times and use the average value, unless some of the values are absurd. Errors can obviously arise from the initial focussing or during the dot confirm. I would not consider a series of AFMAs of say for example 2, 6, 4, 3, 3, 0 to be wrong but merely a mean of 3 with a not unsurprising standard deviation.