Colonel Sam Synn (Joe Flanigan) quips "We're going to need a bigger boat.", an homage to Jaws (1975) where that line became famous.
The soldiers fire an inordinate amount of ammunition given that they cannot know if/when they'll ever have replacements to reload.
Dr. Karen Fast says "That felt like we were sliding.", a play on cast member John Rhys-Davies' role in Sliders (1995) which was also based on alternate universe travel.
This isn't the first time John Rhys-Davies has been a part of something dealing with alternate (parallel) dimensions. He starred in the television show Sliders (1995) as Professor Arturo. The whole premise of that show dealt with parallel dimensions.
At 1:26:18 we see an American flag with 48 stars which was updated to 50 stars following the admission of Alaska and Hawaii. This 2011 movie shows the older version.