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It might be easier to see with a smaller subset of data. From the screenshot below, I've highlighted IDs that should all be grouped together under Group ID 126 because they have a common variable present either under ID #2 or ID #3 (NSLP000003289).
However, the items highlighted in orange are being grouped incorrectly. The idea is if the ID exists within the ID #2 group or within the ID #3 group elsewhere, it should be included with the previously existing group.
Please let me know if there's anything else I can clarify. Thank you!!