is there any contradiction between the two?
IIRC, Jahn-Teller distortion applies only to complexes formed from d-orbitals, not the s- and p-orbitals used to form the bonds in methane.
Jahn-Teller distortion happens in any system where the ground state is degenerate and that degeneracy can be broken by lowering the symmetry. I'm not so familiar with CH_4, but from what I remember from general chemistry, I don't see that the ground state would be degenerate.
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