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While there is software that tries to track adsense ad clicks, it doesn't work with the google server or systems and therefore will inevitably be different. Google presumably filters out duplicate clicks, clicks that cancel (hit stop), clicks that seem like fraud and so on and so forth based on internal business rules which your tracker has no insight into. There are also click attempts that fail and simple differences in what is counted as a click. Ultimately if Google can't charge an advertiser, you can't get credit for a click regardless of that another tool may tell you it measured.
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