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.
Round Cores in the original, when they're fully open. They release projectiles which spin around, soak up quite a few damage and can overwhelm the player.
Also, for normal aerial enemies, purple Lusters which fly around with a wise arc and that means usually firing its projectiles behind the player.
Jack the Dynamic Difficulty high enough and you get these annoying blue enemies that line up with you and shoot out a constant stream of missiles. Flying above them will NOT help because they can fire upwards too.
Game Breaker: Weapon 7. Fired fast, could move left and right at a limited angle, and could go through enemies. Very powerful, but is also a bit of a rarity.
The FC-Custom in Neo. It's basically an Homage to the original Zanac fighter that is unlocked through either a code or having a save file of the original Zanac game, and it plays exactly like the original down to the weapons degradation system, so no blast mode or charge shots. However, all of its subweapons can destroy enemy shots, and this is a ship that, with weapon 7, can rip the crap out of anything. For reference, the regular Neo ships can only destroy enemy shots through sacrificing offense for defense, something that ramps up the Dynamic Difficulty. Oh, and it benefits from the Landers, having an insane rate of fire if exploited right.
Weapon 6 in Neo is an explosive that shreds most enemies and lingers long enough to take out multiple targets, but is extremely slow and the firing rate is abysmal. Power it up to max, though, and you get a massive Sphere of Destruction that wrecks everything it touches (including bosses,) and the firing rate problem can be solved by just getting up in your target's face and unleashing it point blank.
Goddamned Bats - Although many of the enemies qualify, T-Cells, which appear in Areas 8 and 11 in the original game, are perhaps the best examples. They cannot be killed with anything that doesn't clear the screen, they block shots completely and have to be destroyed by bumping into them.
Goddamned Boss - Capital ships in the original game since almost all projectiles bounce off of it (although still damaging it), lowering your fire rate considerably. In addition, all but one of those will actually home on ship.