Sometimes the designer of an experiment can miss the obvious. If your measurement method is not the cause, try to determine if the error is systematic or random. Random errors are more obvious. They result in non-reproducible data that doesn't make sense. In this case, runs with the same combination of variables, and even the control itself, cannot be duplicated.
Some randomness is always present in nature.
No two measurements are exactly the same. You must judge if the differences in your data can be explained by nature operating normally. A random error may be occurring because you are doing something differently in each run. For example, you are not careful in cleaning your reaction vessels and some of the chemicals are being carried over from the last experiment. Scientists use various statistical tests to determine if the difference between runs is due to randomness in nature, or to the way they are doing the experiments.