Update: It's definitely the GSI bot. It has trouble staying in the room and interacting with targets. It keeps falling through the floor or jumping around the area. If this happens while it's attracted aggro, it breaks the fight. And there's no way to dismiss it.

I'm not sure if it's just a solo bug, since I never did the flashpoint previously, but so far it's been a glitchy ride. As mentioned in this thread, the initial commanders didn't all spawn and the phase had to be reset. I've noticed that the GSI bot has trouble keeping up, and tends to pull fights even when stealthed when it tries to catch up. It may have combat issues too: I noticed fights resetting a couple of times (NPCs going to "evade" mode and healing.) I didn't think much of it, but now Darth Soverus keeps vanishing mid-fight and resetting the encounter. I'll keep trying to fight him, but it seems to be happening whenever he's targeted the GSI bot. I don't know if the bot is clipping in the rooms wrong or something, but most of the combat glitches seem centred around it.

I had it happen to me on the Republic solo version. Only 3 commanders.