Continuity: at the beginning of the episode after the credits it shows Scully shoot twice where in the last episode she only fired once.
Although Agent Pendrell's first name is never revealed. In the X-Files game, it is revealed to be Sean.
21:54 When Max yanked out of the plane, when the shot of him is from the window there is a visible safety landing pad on the floor of the set.
Why wasn't Scott Garrett returned after being abducted like Mulder said Max would have been if not for the UFO being shot down?
In 'Tempus Fugit' Mulder and Scully note that all the watches on the crash victims are 9 minutes ahead of the reported crash time. After Mulder's plane is intercepted in this part he sees that his watch is 9 minutes behind Skinner's watch.
Now to decide which is correct and which is the goof.
It makes more sense for the watches to be ahead because the aliens would have stopped time everywhere except on the plane so the watches would still be running, and then the aliens erased their memories, making those nine minutes "lost".
If Mulder's watch was behind in time then it means that time stopped only on the plane, but if that is true then why the need to erase everyones memories? This also goes against the events of the Pilot episode where Mulder and Scully lost nine minutes in the car and Mulder's watch is shown as being fast.
Mulder: I left a bag here.
Security Officer: Big bag, little bag?
Mulder: Small bag, tall bag.. Small bag I think..
Scully: All I know is that this plane seems to be killing people as it sits there on the ground.. Mulder. Agent Pendrell is dead
Scully: Shot. In an attempt on Sergeant Frish in Washington he saved his life Mulder and maybe mine
Mulder: Scully.. Scully
Scully: Mulder what are these people dying for? Is it for the truth or is it for the lies?
Mulder: It's gotta be for the truth, if we owe them anything it's to make sure of that
Scully: (To Pendrell) We've got paramedics on the way you're going to the hospital, you're going to be ok. Look, we still haven't celebrated my birthday Pendrell. I'm not going to let you off the hook like this
Mulder: I think I'm gonna miss the in-flight movie and it's something starring Steve Gutenberg.
Scully: This gift that you gave me for my birthday. You never got to tell me why you gave it to me or what it means... but I think I know. I think that you appreciate that there are extraordinary men and women and... extraordinary moments when history leaps forward on the backs of these individuals... that what can be imagined can be achieved... that you must dare to dream... but that there's no substitute for perseverance and hard work... and teamwork... because no one gets there alone... and that, while we commemorate the... the greatness of these events and the individuals who achieve them, we cannot forget the sacrifice of those who make these achievements and leaps possible.
Mulder: I just thought it was a pretty cool keychain.
Mulder: Do you know where she is?
Scully: In a mental institution.
Mulder: I'd go with you... but I'm afraid they'd lock me up.
Scully: Me too.
Although this episode (and Part 1 "Tempus Fugit") deals with a military cover-up of a downed UFO and elimination of evidence that Max was carrying, it curiously did not involve the Cigarette Smoking Man. This type of work would be right up his alley.
The song that plays when Scully turns on Max's stereo is 'Unmarked Helicopters' by Soul Coughing, featured on the X-Files album Songs in the Key of X.