It's a hold over from the older script for the movie. In it, Rogue is nowhere to be seen. Storm and Cyclops are there to stop Sabertooth and rescue his target. Wolverine. Whom Magneto wants due to the Adamantium in him (and apparently his little dog tags too).
Max "Magneto" Leshner explicitly says that Xavier has been using Cerebro to mess with Magneto's plans:
Magneto glances at Storm, then Cyclops.
The two in Alaska. Just how do you
people manage to be in the right place
at the right time? Still tinkering
(referring to Logan)
What do you want with him?
Magneto smiles now, tapping his METAL HELMET.
Can't read my mind?
Of course this version is a tad different than the final. Erik, I mean Max and Xavier don't have that touching "en guarde" moment at the beginning of the film. Logan is the energy source for the machine. Rogue saves the day. But considering that we know Xavier uses Cerebro to locate mutants and read minds at a distance, this is still proof.
In another version, Xavier was supposedly just looking for Logan, even though Sabertooth still thinks they know:
How did they find me, anyway?
I make it my primary interest to find the
mutants with the most extraordinary powers.
The best potential. We've been tracking you for some time.
Impossible. I would have known.
Xavier taps a finger to his temple.
The mind leaves no tracks/ breaks no branches.
In the final movie when Sabertooth surmises that they knew, Magneto blames Charles without any explanation. Charles says he doesn't know what Magneto was planning due to the helmet. So it's a plot hole in the final cut.