This latest patch seem to increase the difficulty of the NPC Bosses in the Starbase Incursion mission. The Boss meleed my character to death with one blow. I had full health and full shields which didn't matter. The same was happening to my teammates after I was killed. I think that is quite ridiculous that you made the tuned bosses like they were fighting some Pro PVP team or something. These are regular players in these fleet missions. You don't need to test the system with your "Code Cracked Commandos" so you can breeze through the mission. Use regular unbuffed characters to test these missions. Most don't have access to the latest and greatest gear yet. Many of us still have a tier 1 station. Besides we are not fighting monsters, we are fighting a captain, even though the Gorn Captains are the size of monsters. A Klingon captain killing you by boping you in the head one time? What is this "James Bond", "Austin Powers," Judo chop to the shoulder and you're out for the count?
I do this mission several times a day and it is far easier than Colony Invasion. The final boss is actually way too easy compared to the 4 protected saboteurs. I have never experienced what you are describing.
I'm still seeing Incursions with 20+ on phase 1, all four nailed on phase 2. Phase 3, I've very, very, very, very, rarely gotten the Captain. We have time for one shot on the captain, at best, usually missing it because one NPC or another finds a nook we just can't get to quickly enough. The timing on Phase 3 is very unforgiving.