This code causes a Core Lint error:

{-# LANGUAGE TypeFamilies #-}

type family F a b where
  F (Maybe a) [a] = Int
  F b c           = Bool

data Proxy a = P

type family G

foo :: Proxy d -> F d d -> Bool
foo _ = not

bar :: Bool -> Bool
bar = foo (P :: Proxy G)

The solution needs to freshen variables before doing apartness checking. I will fix in due course.