You may be thinking of Starhunter (2000), in particular, Season 1, Episode 19, "Bad Girls".
Starhunter tells the story of a bounty hunting ship, The Tulip, and it's crew: Dante Montana (captain, right), his niece, Percy (engineer, middle), and Lucretia Scott (security, left). Dante and Percy became bounty hunters after their colony on Titan was destroyed by Raiders, and Dante is obsessed with finding his son, who had been kidnapped during the raid. Luc is a member of a shadowy organization, and has her own secret motives for joining the crew.
In "Bad Girls" (from IMDB):
Dante agrees to transport Rudolpho's friend Stephen Hamilton and his two daughters Ayla and Cordula. However, Dante is unaware that Hamilton is being blackmailed by the Orchard to spy on him. Meanwhile, Percy befriends the daughters and clashes with Dante over a new addition to the Tulip's security system.
The episode begins with Percy "upgrading" the ship's loading bay with an automated gun turret for increased security when escorting bounties to the holding cells. The turret's IFF software proves to be flawed, prompting Dante to chew her out and demand it be taken offline.
At the end of the episode, the Tulip is forcefully boarded by shuttle through the loading bay, but the turret, which had not been disabled (or had been reactivated) proved successful in taking out the boarders.
Here is a blog post outlining the episode in detail with some screengrabs. There aren't any photos of the turret itself, but I recall it looked like a trash can mounted on the ceiling horizontally (which provided vertical pitch), with two gun barrels (that could angle horizontally) coming out of it. The post does have a photo of the boarders (dressed in black riot gear) getting shot up, though.
Edit: I just remembered, full episodes are available on YouTube; I won't link them since I'm not sure how legal that is, but here's a screenshot of the turret:
There aren't any aliens in the show, but one of the greater story arcs involves alien influence on human evolution, and this episode touches on that theme a bit. Additionally, the ship has an AI named Caravaggio, whose holographic avatar is somewhat strange looking.