I believe it had to do with Mahito's specific nature. The "You can't hurt me unless you hit my spirit core" and something about his special punches allowed him to strike through to his spirit core.

And also the whole "I can't shapeshift his spirit or Sekuna will fucking kill me" bit.

So A. He can't use his main ability on him, and B. He has attacks that can actually hurt him. Just an overall bad matchup.