I have tried this on multiple character types with multiple ships.
Most recently trying my temporal character sci capt (advanced) with the Krenim sci ship, trying to grav well/tract beam them, then Nandi ship with web / chron mines laid out after the first ship appears, before the first wave. I also had grav well and scramble available.
There is always a ship or two that sneaks by. It seems the closer they get to the entrance, the easier it is for them to ignore your control effects.
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EDIT: Also, GW is more effective the higher your aux power levels.
With unaltered aux base of 103 in the Krenim sci vessel, I watched as a ship, like a football player slipping through the last few yards to the goal line, ignored my gw3.
The Krenim science vessel has a Lt. Commander Tac/Intel seat, which means it can use Override System Safeties 3. If you equip the Chronometric Polaron set from Time and Tide, you can combine OSS with the set power for a massive boost to weapon and exotic damage. The Krenim Chronometric Torpedo makes this boost last longer.
I think I've gotten this accolade on at least one toon by just pouring in weapons fire and big torpedo spreads once the portal's shields are down. For a science captain with high EPG, the Particle Emission Plasma Torpedo may be a good choice, and the Neutronic Torpedo is part of the set that grants the Isokinetic Cannon power. The energy weapon side of that set is Polaron-based, so I usually combine it with the Chronometric set on my sci captains.