I am showing an "empty" notification on The Tower in the Director screen, for two of my Guardians (i.e. the outward radiating diamond, the centre of which is empty).
I think this is probably because I have taken a new ship out of the vault with both Guardians before collecting my refurbished ship from the Shipwright.
Only a minor bug, but thought I'd report it anyway!
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Is it your two lower level characters? Do you have the Dark Below? An empty notification icon will appear for lower level characters on accounts with the Dark Below. It is an indicator of Eris's expansion quests. You can clear the icon when you reach your 20's, and take on the expansion bounties.