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I just beat the level and got all three discs on that single play through. Since I don't know exactly which one you're talking about, so I'll just list all three. These are from memory, so it'll be about as descriptive as I can. I've omitted the names on purpose.
One of the three discs requires a flying Decepticon and is mid-air while the first Autobot, the one that is shooting the plasma shots, is shooting at you during a chase sequence. The second one I remember also may require a flying Decepticon and its in a room that requires you to hit three switches. There are a ton of swarm enemies in this room, but when you first enter, it is located on the right, partially hidden in light. The third is right before you fight the flying Autobot boss, the one that shoots the missiles at you, and again is located in a chase sequence, this time, you can only see it if you turn around once you get to the end of the corridor (the room has random explosions and missiles coming from the sky.
Let me know if that was descriptive enough to help. If not, I can try to replay the sequence and be more detailed.