Oh that happens with Purple star systems, something to do with the part of the Glyph Address portion that denotes a system. I think anything above the number 400 (for arguments sake) was unused until they added purple star systems.
They’re still invisible/inaccessible for those without an atlantid drive even if they have the portal address so I think it’s a holdover/disclaimer tied to that which is being emulated on the Haven Map.
I mostly submit purple star systems so it’s a handy indicator for me that I definitely entered the glyphs right. And I enjoy seeing the spooky ghost emoji 
The folk over at VHAV gave me a better understanding of how the portal address’s work by showing me this, and this image is also the basis for how they started to understand the glyphs and construct the map.
I went back and checked the chat logs to be sure…
Ekimo who codes the map said this in regards to the phantom system warning
“Yea it’s a known thing. I only went up to 600 ssi and purple systems are above that”
So there might be a few non purple star systems in the mix there too for a spooky ghost message. oOOooOOoOOooo
And don’t worry, this glyph cube also hurts my brain :-S
The most interesting thing to me that I can decode is that 0 is always 0 and then 1-7 and F-9 are negative or positive numbers depending on the axis.