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Spoilers, of course.

Towards the end of Season 2 of The Expanse when the Rocinante is about to leave Tycho for Ganymede, Fred Johnson tells Holden they're no longer welcome on Tycho station.

Why did Fred say this considering that both groups worked together, the Rocinante crew just saved Fred from the Belter gang and that Naomi secretly gave Fred the location of the hidden proto-molecule torpedo?

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... and that Naomi secretly gave Fred the location of the hidden proto-molecule torpedo?

Exactly this has not yet happened at the moment of the Fred-Holden conversation (S02E08); only in a later episode does Naomi give away the location of the protomolecule sample. And the protomolecule is indeed the motivation behind Fred's "hostility": Holden is heading to Ganymede to destroy it, but Fred wants a piece of it for himself/the Belt:

FRED: I don't have to let you leave, you know. With all the time and repairs I put into this ship, it's arguably more mine than yours.
HOLDEN: We just saved your life. Call it even.
FRED: I know we've had our differences. But if you find the protomolecule on Ganymede Station...
HOLDEN: I sure as hell ain't gonna bring it back to you.
FRED: Then don't bother to come back here at all.

Transcript from https://www.springfieldspringfield.co.uk/view_episode_scripts.php?tv-show=the-expanse-2015&episode=s02e08

Edit: While re-watching, I stumbled over the bit where Naomi tells Holden when she gave the location to Fred (in S02E13):

There was a moment on the Somnambulist when I thought I wasn't going to make it [...] I gave the protomolecule to Fred Johnson.

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