The number one mistake I see people make is measuring one time and taking the results at face value. If you do nothing else, measure three times and you will at least have a feeling for the variability of your data. If you want to compare two versions of your code with confidence there is usually no way around proper statistical analysis.
Which brings me to the second mistake. When measuring runtime, taking the mean is not a good idea. Runtime measurements usually skew heavily towards a theoretical minimum which is a hard lower bound. The distribution is heavily lopsided with a long tail. If your objective is to compare two versions of some code, the minimum is a much better measure than the mean.