I'm having this problem as well, only the logo (which should be a fingerprint) has turned in to a totally black circle on the different floor plates/banners, which I guess would be the filled in biohazard symbol.
This bug has also been mentioned in the Base Construction section of the forums, along with a load of other bugs.
Help Dirk Knightly the freelance detective solve a case in Arc ID:368097
Right now all base details that show a supergroup logo (banners, floor tiling etc.) have changed to show the biohazard symbol and cannot be reverted or changed to anything else.
Also pre-existing VEATs cannot run any of the new Mercy Island missions via ouroboros as Operative Kuzmin simply directs them to speak to them to Alan Desslock and they are unable to start the arc.
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9/13 - Never Forget.
8/31 - Never Forget even more.