Can we just first please verify how you opened the Score Editor?..
Did you just select multiple MIDI Tracks (some of which didn’t have any MIDI Parts on them)? If so, then what you describe is normal. For a staff to appear in the score, there has to be a MIDI Part for it, even if the MIDI Part itself is empty.
If you did all that correctly, then I’ll have to have another think 
- I would like the Bar Numbers to be automatically set to the Left of, or even Centred on the Clef Signs
Score Settings menu (or the “I” icon in the extended toolbar)>Project pane>“Notation Style”>Bar Numbers>
Two things to do…
- Show every “First Bar” (or can type “0”)
- First Bar Number to Barline (checkmarked)
You can further refine this by
Project pane>Spacings>First Bar Number - Horizontal offset (and, of course, vertical too, if you wish
.