Only the calls that involve non-judgment can be challenged. Usually, the only non-call plays that can be challenged are the penalties that involve too many players on the field since it is able to be seen on the replay.
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Only those calls that involve 'non-judgment' can be challenged. And, as far as I know, the only non-judgement call that can be challenged is too many players on the field since it can be absolutely determined, by the replay, how many players were on the field at the time the ball was snapped.