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.
The small spider creatures that latch onto Duke (some even fall from the ceiling) and drain his health until you shake them off
The slug-like creatures that throw their eyeballs at you, then explode into a shower of eyeballs when you kill them
The ships that fly overhead and drop bombs with a rather huge blast radius; if you don't have anything besides the default weapon you're practically guaranteed to get hit (and even if you shoot the bomb as it's falling, it blows up anyway and the explosion will probably travel downwards far enough to still hit you)
The panther-like creatures made of green slime
The small ships in the first level of episode 2 which don't appear until you're practically on top of them
The hopping one-eyed robots.
Scrappy Mechanic: Red boxes contain either health pickups or bombs, with far more of the latter than the former. For extra screw-you points, they're frequently placed right next to actual health pickups, which they'll promptly destroy if you don't scroll the pickup box off-screen so that the explosion doesn't affect it.
That One Level: The first level of Episode 4, where you're hanging on the outside of a spaceship leaving the atmosphere, jumping from ceiling bar to ceiling bar, and one misstep will have you falling to your death.