The discrepancy occurred because the Apsona report did not include a unique identifier field like Record ID.
Apsona automatically deduplicates results when fields such as Name (which may repeat across records) are used without a unique field.
As a result, multiple leads sharing the same Name appeared only once, reducing the total record count.
To fix this issue:
Edit the report columns
Add Record ID (or any unique field)
Re-run the report
Once Record ID was added, Apsona returned the full dataset, and the result matched the SOQL count.
Key Takeaway:
Always include Record ID when validating or comparing data volume or when exporting, it prevents auto-deduplication and ensures all records are returned.