I just read the USA Today article (link posted somewhere above) and it mentioned that a second study was conducted to check the overvotes, but hadn't been completed when the article was published. The overvotes were ballots where more than one name in any given race was selected (not just for President), thereby automatically disqualifying the entire ballot. There were 110,000 of these and Franken may be referring to this recount for the entire state. But if a ballot is invalid because two people were picked, then they should never be counted. SCOTUS disagrees in the USA Today article.
There were also some that filled in 3 of the 4 straight party bullets - so nothing counted.