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Are the spikes of long enough duration and frequent enough that you won't be getting the correct answer from the modeling results at a holistic level?

It will depend on what you are trying to get out of the model -- if you are trying to optimize other parts of the building, maybe these spikes don't change the larger recommendation.

However if the analysis is specifically pertaining to the zone airflow and OA quantity, then I think you need to review the parameters as suggested by Mike Witte, and/or investigate the possibility of a bug.