I've noticed that there are some units without triangle counters, which are intensely annoying to face in any game. Countering them essentially relies on luck of the draw in bonus units, or simply throwing starships at them. I don't really know if this is intended or not.
Electric Bombers: The most notorious owing to the 'strong fleet ships' issue. However, even ignoring that, they hard-counter Bombers, which have a (small) bonus against Heavy.
Units with Composite Armor: For example, the Z Beam Frigate. Composite armor is rare, but virtually nothing has bonuses against it. There isn't even a turret type.
MLRS: The principle counter to Medium armor is the Fighter. Unfortunately, MLRS groups tend to leave small smears where Fighter groups used to be. MLRS are also hard as nails, with lots of hit points and tough armor. The only real bright spot is that their per shot damage is too low to hurt units with armor. The only effective counter I've found is Mk 2 Riot Starships, which can sit on a group and kill/permaslow them using tasers. To be honest the Riot Starship tactic is overpowered, but I've got nothing else that works on MLRS besides sitting there and bashing them for 15 minutes with starships and bombers.
Deflector Drones: Same as the Electric Bomber and MLRS, Deflector Drones hard-counter their triangle counter, the Missile Frigate. Deflector Drones have extremely low HP however, so they can be killed effectively by Fighters and Bombers. It's just kinda weird that your best counter to this unit isnt what the hull type bonuses lead you to believe.