User warnings can be deleted in the MCP. To be able to do so, the MCP lists all log entries from the specified user. Marking one or more entries and then clicking on "Delete" will remove the log entries AND the entries in the warnings database table.
However, if an administrator is deleting log entries in the ACP and he also deletes one of those warnings log entries, the log entries will be deleted without removing appropriate warnings database table entries aswell.
Either /includes/acp/acp_logs.php must consider to also delete warning entries aswell, or /includes/mcp/mcp_notes.php must expect missing log entries when listing options to delete from (speak: select from both logs and warnings).
The current behaviour is a disaster for those not being able to manually manipulate phpbb_users.user_warnings and phpbb_warnings but keen enough to "just" delete log entries.