The layer in the (.mpkx) file has an invalid definition query.
For example,
tableName.FieldName = 'tableName.FieldName2'.
Remove this definition query and reapply it using the query builder UI as
tableName.FieldName = tableName.FieldName2.
This is tested and works in current versions of ArcGIS Pro 3.3 and 3.2.
Note: In ArcGIS Pro 3.2, many bugs with definition queries working with joins are fixed. This may be valid in prior releases.