The Holy Grail from Indiana Jones and the Last Crusade (1989) can be spotted among the items in Thrawn's collection.
In Thrawn's office, there appears a relief on the wall showing two lizard-like creatures. Dave Filoni confirmed that these are a deliberate nod to the "Heir to the Empire" trilogy where Thrawn wears Ysalamiri on his shoulders to nullify the effects of the Force. Ysalamiri will not feature in Rebels.
Dave Filoni toyed with the idea of having the entire episode be told through Agent Kallus point of view, but this soon proved to be too difficult to produce so he had to settle for just the opening scene.
Thrawn utters the override code 'Rukh' to stop his Imperial sentry droids. Rukh was the name of his personal Noghri bodyguard in the Thrawn Trilogy of books ('Heir to the Empire', 'Dark Force Rising' and 'The Last Command') which are no longer canon.
Tom Kane reprised his role as Admiral Yularen from Star Wars: The Clone Wars (2008). During the Clone Wars, Yularen was the admiral that served alongside Anakin Skywalker and was usually seen on the bridge of Anakin's Venator, the Resolute. As the Empire rose, Yularen was made a colonel leading the ISB, the role he holds in this episode. This foreshadows his appearance on the Death Star in A New Hope.