The nature of the challenges (e.g., voter intent is clear, identifying mark, etc.) that Franken and Coleman are putting up differ.
In general, there were more Franken ballots that the machine wrongly threw out than Coleman ones. For example, if a voter selects Franken, but then scribbles out Coleman's name and bubble, it would register as an overvote, even though the hand count would count it for Franken (based on the obvious intent). Coleman voters were less likely to do that.
Don’t panic yet. Withdrawn challenges are not yet clearly in the count. Franken withdrew many more than Coleman. They’ll be added back eventually.