As I mentioned last year around this time, it is possible to end up with passes that don’t show up in the explorer. This happens when you Duplicate a pass, and the Hierarchy option “preferences.duplicate.hierarchy” is set to None. So your new pass has no parent, and is disconnected from the rest of the scene (aka floating).
These phantom passes have names like “#Pass”, and you can select them if you know how.

Here’s how, in Python, with the 2013 SP1 Python shortcuts.
from sipyutils import si # win32com.client.Dispatch('XSI.Application')
from sipyutils import siut # win32com.client.Dispatch('XSI.Utils')
from sipyutils import siui # win32com.client.Dispatch('XSI.UIToolkit')
from sipyutils import simath # win32com.client.Dispatch('XSI.Math')
from sipyutils import log # LogMessage
from sipyutils import disp # win32com.client.Dispatch
from sipyutils import C # win32com.client.constants
si=si()
sClassID = siut().DataRepository.GetIdentifier( si.ActiveProject.ActiveScene.Passes(0), C.siObjectCLSID )
passes = si.FindObjects( None, sClassID ).Filter( "", None, "#Pass*" )
print passes.Count
print passes.GetAsText()
#
# The following don't work! At least not all the time 😦
#
si.DeleteObj( passes )
#si.ParentObj( "FloatingPasses.Passes", "#Pass<61>" )
#si.CopyPaste( passes(0), "", si.Dictionary.GetObject("FloatingPasses.Passes") )
si.SelectObj( passes )
When I was testing this, sometimes I was able to delete those phantom passes, and sometimes I wasn’t.
Sometimes those passes disappeared when I saved the scene, did New Scene, and then reloaded the scene. Sometimes they didn’t (disappear that is).
When DeleteObj didn’t work, I’d use the explorer to view the phantom passes (since I called SelectObj on them, I could just show selected in the explorer).