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marvin the martian

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You first have to make contact with the empire it belongs to (via a society-project) before you can take a look at their specs.
However, if the strange vessel turns out to be a space creature (amoeba, void cloud, etc., including the generic pirates), you don't get the option to scan them at all.
 

Wyrm

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Possibly because the scanners can't make sense of it?

Ships belonging to non-standard entities (Empires) are unscannable. It adds a bit of mystery to some of the strange creatures and vessels you encounter.
 

The Founder

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You can not see the Layout of a ship, before you Contacted the owners. And for many event/special ships/special empires, you can never see the layout.
Note that there is still a layout wich can be read out of the gamefiles. Indeed that is where we get most of the Wiki-data on the ship layouts.