"Because the supplemental opinion was late, it was not allowed. Could it be that it's material wasn't needed anyway for a rebuttal of the request for Summary Judgement, and that if it were not thrown out being late could give grounds to the infringers for a 'down the road' appeal of some sorts? I can see the courts opinion taking such things into consideration."

I know nothing, but I agree that your scenario is entirely possible. It seems unlikely to me that the judge and his staff could evaluate and reject the supplemental opinion, based on its content so quickly. The question remains, as you say, is it needed?