In Season 2 Episode 9, "Going out Fighting", the "black goo" appears to be a sentient "alien" being. The following article does a good job of describing what happens:
Three wakes up in a cell in the infirmary. He demands to know what’s going on, then tries to shift blame to Six. Android says that although Three is awake, his neural activity is more consistent with REM sleep. Two tells Three that Rook must have done something to him, and that she’s not going to let him out until she knows what. Suddenly, the black smoke curls across Three’s eyes, and he begins to convulse. He begins to scream, an inhuman, demonic sound. Two has Android drop the shield that forms the front of the cell, and shoots him with another knockout bolt.
Two decides to put Three into a stasis pod until they can get back to Earth to find out what’s inside him. Despite Three being unconscious, his eyes pop open, and he screams again. Thick black goo streams out of his nose, eyes, and mouth, straight up to the window of the pod. Whatever’s inside him is trying to escape. They drag the pod into a hallway next to an airlock, open the pod, and drag Three away from the goo. They then seal off the corridor in front of them and open the airlock, sucking the thing into space.
According to Wikipedia there are also aliens in Season 3 Episode 11, "The Dwarf Star Conspiracy". I haven't seen the episode but from the description these sound like the same aforementioned ones.
The Raza crew, joined later by a Mikkei ship, investigate a seemingly abandoned Dwarf Star Technologies lab and find many "simulants"—bio-synthetic organisms like Two—in stasis, as well as a mysterious anomaly that induces a violent mental disturbance in Three. Hostile aliens from another universe accessible through the anomaly, speak to him (in a prior episode, he was possessed by one of them); he learns they plan to leave their dying universe and use the simulants as host bodies for their invasion. The Mikkei second-in-command, who turns out to be a simulant herself, assassinates her commander and opens the anomaly to allow the aliens through. To stop them, the senior surviving member of the Mikkei landing party calls for a nuclear strike on the lab, then kills himself, leaving Two alone in the lab. The Raza crew are unable to stop the bombing. At the last minute, Two is kidnapped by the alternate universe Boone and flown away in his FTL-capable Marauder.
These then resurface in Season 3 Episode 11, "Nowhere To Go". Thanks to joeytwiddle for finding these and commenting below.
Before Two can kill Ryo, Teku offers the location of the secret Ferrous shipyard in return for his emperor. Traugott, allied with Mikkei, provides a white hole bomb to destroy the facility, but it is a trap: the bomb is a dud, and Two, Three and Six are captured. Alternate universe Wexler—secretly working for Mikkei—helps them escape, but Three is recaptured. Moreover, unknown to the others, Two has been possessed by one of the aliens from "The Dwarf Star Conspiracy". Truffault provides all the ships she can scrape together; they, along with Teku's loyalist Ishida fleet, attack the facility, but Ferrous's defenses are too strong. Portia Lin escapes in the chaos, taking Three with her. Two proposes destroying the shipyard by transferring the blink drive to the Marauder, taking it in close and overloading the drive. The Android, incapacitated by Two, still manages to warn Five that Two has been compromised, but she is too late. Six detonates the blink drive, apparently annihilating the shipyard (and himself), but a giant spatial anomaly forms, and huge black spaceships come through it.