At the end when Ultra Magnus says, "This nova will be his memorial," it is Rodimus Prime's mouth which is moving.
Optimus Prime's damage varies greatly from scene-to-scene in this episode.
During the battle with the Quintessons, several Aerialbots (or,more likely, Aerialbot lookalikes) are destroyed.
Rodimus refers to Optimus as having been dead for years. Since he died in The Movie, which took place in 2005, and this series took place in 2006, Rodimus is really exaggerating the length of time.
When the Decepticons are flying towards the mauseleum, there are two of Dirge!
Nothing happens to Hot Rod when Optimus Prime gives him the Matrix.
Optimus Prime: Until all are one.
Hot Rod: Ha ha. Fooled you!
Optimus Prime: Not a game, Rodimus. Matrix... makes me... too... strong!!!
Hot Rod: There's a unique complaint!
Optimus Prime: If you loose, Autobots, all, destroyed!
Optimus Prime: Optimus Prime to Autobot fleet. Return to Cybertron, that is my 'final' command.
Rodimus Prime: Optimus? What are your commands, Sir?
Optimus Prime: Is it safe?
Rodimus Prime: What? The Matrix. Yes, I've been keeping it warm for you.
Ultra Magnus: Wait, Optimus is in no condition to assume leadership.
Rodimus Prime: Come on Guys, he's just shook up a little. You'd be too if you've been dead for years.
Kup: That's the point, Sonny...
Rodimus Prime: I don't want to fight you!
Optimus Prime: Then stop me!
Optimus Prime: Monsters. They made me a weapon to destroy the very ones I loved in life. But you will save them, Rodimus Prime.
Optimus Prime: You should have finished me!
Rodimus Prime: Believe me, I tried
Oprimus Prime: Until all are one!
Rodimus Prime: If he were alive, I'd know. The matrix would have told me; some how.
Galvatron: How convenient, Rodimus. We can lay your wreckage beside that of your mentor.
Rodimus Prime: I don't know if I'll ever be the leader that you were, but for sure, I'm going to try. So long, Prime.
Wheelie: The dead do not drive! Rodimus is alive!
Ultra Magnus: There are too many Decepticons!
Kup: One Decepticon is one too many!
Optimus Prime is missing his Autobot logo from his left shoulder (19:48).
The ship given to Galvatron (and subsequently destroyed) by Unicron in Transformers: The Movie has either been repaired or replaced.
Since the Autobots won the Great War, why are their fallen heroes floating around in the middle of space while the Decepticons, who lost, have a crypt right on Cybertron as we find out in the next episode, "Starscream's Ghost".
After this re-episode aired (the day before Return of Optimus Prime aired) this was the stated:
"But is this really the end of Optimus Prime, find out in tomorrow's exciting episode The Return of Optimus Prime"
There were two different verisons of this episode made; One with the current ending where Optimus Prime flying into the sun and dying. And the other version had an alternate ending where Dr. Swafford and Jessica Morgan rescue Prime before his ship explodes which was shown the day before "The Return Of Optimus Prime" aired!
It appears that Huffer was killed in the movie during the Decepticons attack on Autobot city since we see his tomb on the grave ship.