When Phil Coulson admits that Fury's Toolbox contains no information about human outposts in space, Yo-Yo Rodriguez replies, "S.H.I.E.L.D. doesn't have a space division called S.P.E.A.R. or something?" which Coulson declined. This is a reference to S.W.O.R.D., a S.H.I.E.L.D. subdivision specialized in extraterrestrial threats in the comics.
Jeff Ward was originally cast as Virgil, a character who only appears in a few scenes, but made such an impression on cast and crew during the table-read that they decided to have him play the recurring character of Deke instead.
Virgil refers to himself as a "true believer." Stan Lee would address Marvel Comics fans as true believers.
Yo-Yo makes reference to S.H.I.E.L.D. having people on the Moon. Inhumans (2017) took place on the Moon.