I mostly reported this on the Unthemed Weapons Collection page, but I'm putting it here as well:
Phase Anchor as a default equipment on NPC ships can create some strange / wonky situations. I had to destroy a fleet with a pair of Alcotts, each of which had a Phase Anchor as default gear. Because I had to entirely destroy the fleet, I couldn't let it retreat (it was guarding a fortified cache), one Alcott retreated with its phase anchor and kept coming back. It only eventually died at 0% CR and 0% hull.
I think Phase Anchor probably needs a vanilla tweak, but I don't think it shows up on any NPC ships in vanilla. In any case, worth considering removing it from the Alcott or finding some other way to ensure it doesn't cause problems.