Thanks for using Cloudera Community. Based on the Post, the Phoenix Delete Command is reporting more records being deleted than the Select Count(*) returns. Thank You for sharing the HDP & Phoenix Version as well.
Few Queries for your Team:
Whether the Observation is made for all Tables or Selective Table(s),
Explain Output of the Select & Delete SQL,
Any Index of the Phoenix Table being deleted,
If Performing MajorCompaction on the Table before Deleting (Just for Sanity Check) shows any Difference with respect to the Rows Deleted via Delete SQL.