It seems you are misinterpreting the way in which Coopertition is scored: once per match, very much like the bridge in 2012. The wording of the manual in its discussion of Coopertation supports this.
Quote:
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Coopertition Points are awarded if, at some point in the Match, there are at least four Yellow Totes on the Step simultaneously. Coopertition Points are doubled if the Alliances arrange at least four of those Yellow Totes in a single stack on the Step.
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Emphasis mine.
The 20 or 40 points are awarded on a once per match basis if the conditions were met at some point and for at least 3 seconds in that match, and not per instance of stack formed.
Additionally, the field status light will turn white once a stack has been reached. The match display will also display a symbol indicating the set or stack has been reached.