Wow, what a coincidence. I just picked up my old Metroid Prime game due to a recent craving, and had the same issue in the same exact spot. I simply cleaned the disc and CAREFULLY brushed off the lense with my shirt.

A side note:

Another issue I have with my game is that in certain areas the gamecube itself seems to skip, if this happens stop moving and let the system load more.

I hope this helps!