In Marketing Cloud Intelligence, discrepancies between the number of rows uploaded and the number of rows present in the source file can be caused by several factors. If all mapped measurements for a row are zero, that row may be excluded from the upload, as it does not contribute to the analytics. Additionally, if the main entity, which acts as the primary identifier for records, is not mapped, the system cannot correctly ingest the data as it lacks the necessary reference to organize and store the information.