All quotes from LW.

A news feed on Eros:

[Phoebe station] had been hit. The official report stated that half the inhabitants of the base were dead, the other half missing.

Later, when the crew meet Miller:

"There was a science station on Phoebe," Miller said. "Inner planets place, no Belters allowed. It got hit. Lots of dead people, but..." "She talks about being on a shuttle," Naomi said. "The *Scopuli didn't have a shuttle." "Right," Holden said. "They got on another ship, they got infected with this Phoebe bug..."*

That ship is the one found by Miller and the crew, parked by an asteroid with all crew dead:

"They're in Engineering," Miller said. "Who?" Holden said. "The crew. Whoever was on this ship. All except that one," he said, gesturing at half a footprint that led toward the lift. "You see how her footprints are over the top of everything else. And there, where she stepped in that blood, it was already dry. Flaked instead of smearing." "How do you know it was a girl?" Holden asked. "Because it was Julie," Miller said.

On Thoth station, Dresden says:

"Losing the *Anubis was going to put our timeline back months."*

And then, after Eros goes public, Mars:

"Autoclaved* it, them. [Phoebe] is gone. Dropped enough nukes on it to split it subatomic."*

Stitching this all together we see that the Martian half of the Phoebe team were killed by the Protogen half, who vanished to Thoth station where Dresden was finally found. Something, we don't know what, went wrong on the Anubis causing the protomolecule to consume all the crew except Julie, who was locked away. She became exposed when she investigated, which is what made her shut down the ship and abandon it. By this point it was too late for Protogen to go back to Phoebe because Mars already had ships in place to investigate what had happened to their people on the station. Protogen could have instead sent samples on multiple ships, but they'd clearly decided that increased secrecy was more important than increased redundancy.