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The “Exclude users who did” feature only excludes users between specific steps in the funnel, not from the entire funnel. If a user performs the excluded event after completing all the funnel steps, they will still be counted as converted. If you want to exclude users who did a particular event at any point, use a cohort filter instead.

Unfortunately, it’s not possible to increase the Query API rate limits. Mixpanel enforces these limits to maintain computing capacity and ensure fair access for all customers. To work around these limitations, Mixpanel suggests:

As outlined in the engineering blog, events can be deduplicated if they share the same:

When all four keys match, the events are treated as duplicates, and only one is shown. I understand you now have duplicate events. A workaround is to filter by the backfilled property(is set) when querying the data.