We've seen a few cases where mismatching data in Funnel has turned out to be due to 3rd party data integration within Klaviyo. If troubleshooting and you can't explain the mismatch by the known difference in how data is shown in the Klaviyo application vs. what is returned to Funnel by the API, looking at the metric_id might be an option. See this article Klaviyo - Troubleshooting.
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Reason for the mismatch in these cases has been that a metric name, for instance "Placed Order", has had multiple metric ID's/data sources. The data from both these sources have then been combined in the funnel views due to selection being done by Metric name.

Ex:
Metric name: "Placed Order" - Metric ID: "TTudb8"
Metric name: "Placed Order" - Metric ID: "hdKb5s"
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To facilitate filtering and get only desired data, and for troubleshooting/checking if this is the case, we have made the metric_id available as a field. You find it under Choose fields, by searching for metric id:

Using filters on the column you can exclude or include specific metrics.