When 'Maddie' Madeline (Amanda Righetti) checks the flight status website, as she's ending a phone call with Katie (Sarah Wayne Callies), the flight she is viewing is from the airline "Oceanic." Oceanic is the same fictional airline, Oceanic Flight 815, that crashed in the tv series LOST (2004). LOST also starred Josh Holloway (as James 'Sawyer' Ford), who plays Will Bowman in Colony (2016). Carlton Cuse is also tied to both tv series as Writer/Executive Producer for LOST (2004) and Creator/Writer for Colony (2016).
Broussard's friend is named Wierzbowski. This is the same name as Private Wierzbowski, one of the first marines to die in the film Aliens.
At the beginning when Katie is driving with Jacob in the car she says, "Thank you Hal." Jacob asks, "Who's Hal?" Jessica replies, "he retired." She is likely referencing "2001: A Space Odyssey" where the onboard AI computer is named HAL 9000 (shortened to HAL when speaking with him).