Tried to update Trellis, Bedrock and the vagrant box. And got this error after vagrant up. I get this same error with the current dev master with the out of the box settings etc.
The reason for this is WP 4.6 (works normal with 4.5) - Patch coming up soon - https://core.trac.wordpress.org/ticket/37736
So i would wait a bit with updating WP 
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Do you have this fix: https://github.com/roots/trellis/pull/640
I was getting the same error on 4.6 before I updated WP-CLI. Still not exactly sure why it fixed it though.
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Yep i had it but it still didn’t work. Changed to 4.5 and it worked. WP will fix this in 4.61.
I think there were 2 separate errors and wp cli just fixed one.
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