These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
This will happen quickly if the zombies take over too many of your ships, especially your larger ones, in a short period of time. In those cases, its probably best to do a mass retreat, or Rage Quit, though hopefully you saved prior to getting swarmed on that level.
Big Brother ships, if they're carrying drones. They're the one time where the AI doesn't charge in with reckless abandon. Instead, they'll hang out at the edge of the system and attack whatever the mission objective is with their drones. It's entirely probable for them to take out whatever you're protecting before you've managed to reach and destroy them.
Game Breaker: Several, especially with a loadout that synergizes well with these things:
Mines currently do good damage against all health types, but the broken aspect is that the enemy AI suicidally charges into any dropped mine fields, regardless of enemies nearby.
The Particle Cannon is effective against everything, has minimal power use, and is really accurate. The game knows this, too; the Battle Station deployable turret has two medium Particle Cannons along with heavy armor and shielding.
The leech beam is so efficient that one or two can easily compensate for the heavy power draw of a ship with a fusion beam in all the other slots, without any reactor boosters. It even has longer range than the fusion beam, so if you're hitting the target with a fusion beam, you're hitting them with the leech beam and recharging yourself at the same time.
Many of the bounty hunter ships, as long as you use their over-abundance of utility slots to compensate for their Crippling Overspecialization:
The Claw racks two medium weapons on a tiny hull. It has no utility slots to put reactor boosters on, but the damage you can inflict with it as your number three or number four ship is far more than you could before the expansion.
The Cyclops, a small hull with a huge mount. Unlike the Claw, it does have utility slots, and is especially effective with either a beam or the particle canon. With the latter, you can mount cannon boosters instead of reactor boosters.
The Brute fills the Hammerhead's role but is a Large hull instead of Huge, freeing up your Huge slot for something else or for a Hammerhead anyway.
The Mammoth has about as much firepower as the Hammerhead, more health, more crew, more cargo space, more utility mounts, and a large mass bomb/mines/deploy-able turret mount (deploy-able turrets are especially effective with it). It has six utility mounts, two huge and four large. It can be configured for almost any role and will carry out that role very effectively, be it DPS, siege, rez collection and then some. About its only downside is that it has no missile mounts, so if you want to use it to chase faster targets, you have to put a mass bomb on it.
The Manta Ray has less durability than the Mammoth and has fixed gun mounts, which it makes up for with ten large gun mounts on the front. Remember that bit about the leech gun and how well it works above? Two of them on the middle two gun mounts can drain enough power to supply fusion beams in all the others (the bounty hunters will do this to you). The Manta Ray makes stations (normal ones or zombie equivalents) a breeze, and helps immensely with destroying a Level 4 Bounty Hunter base.
Drones are largely seen this way. The artifact protection mission is basically impossible if one of the UTA ships has them, because they target the artifacts and are difficult to destroy without accidentally hitting the artifacts. Zombies floating in space can be this way too later in the game.
Cloaked ships. This is bad enough for enemies, especially larger hulls which like to pitch gravity missiles from long distances. It is a nightmare for friendly ships, which won't let you see them yet will suicidally charge into your line of fire then blame you for shooting them.