This may be because of "srchIndexesDefault" setting for a user. srchIndexesDefault - is a semicolon-delimited list of indexes to search when no index is specified.
So, if you don't specify the index name in your search, splunk will look at default indexes to search. Hence, inconsistencies in results.
Below is more information of this setting:
srchIndexesDefault =
* A semicolon-delimited list of indexes to search when no index is specified.
* These indexes can be wild-carded (""), with the exception that '' does not
match internal indexes.
* To match internal indexes, start with ''. All internal indexes are
represented by ''.
* The wildcard character '' is limited to match either all the non-internal
indexes or all the internal indexes, but not both at once.
* If you make any changes in the "Indexes searched by default" Settings panel
for a role in Splunk Web, those values take precedence, and any wildcards
you specify in this setting are lost.
* Defaults to none.
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