Okay. Here are some things I noticed about HF that are kind of dark.
DISCLAIMER: I am not nearly as big an HF fan as I am Bionicle. I may have made some errors. I tried to be as accurate as possible, but I am only a (Makuta) human.
1) There is no due process. When the Heroes decide you're a "villain" and they take you, you get put in a shipping container with laser bars (breakout.) There is no trial, and your guilt is pretty much assumed. (Granted, all of the villains I can think of would pretty much admit that they are guilty but still.)
2) Hero Cores might not do anything. In the beginning, there was some jargon about them having to be re-charged, but when the Heroes all went off to a jungle planet for a year, it never seemed to bother them. (Granted, they could've brought a battery with them or something, but when Rocka crashed, he didn't seem overly concerned that he didn't have one.) In a HF pamphlet sent out by Lego in 2010, it is noted that Surge is concerned that his core is flawed, and that Furno's core is supposed to be newer, making him more capable. However, Surge never turned to the darkside, and Furno never did anything super remarkable.
3) The villains killed all of the organic beings. Okay, this one is a bit of a stretch, I admit, but a couple of HF ads ran at the beginning of its run intimated that humans could call HF if they needed. But within the HF universe, there are no pink fleshy humans. The universe is so crime ridden that someone decided it needed a giant factory to build robots to punch the criminals in the face. Before that, where do we think the humans went?
4) Recon Team runs covert ops. Who do we know from Recon Team? There's the Recon mascot, the guy that sported the dual colored chest plate, and spoke all about it. The only other member we meet (I believe) is Rocka, and he's alone when we first meet him. As soon as other heroes show up, Rocka immediately leaves Recon team to join Stormer's team. He never goes back, and Recon Team never checks up on him. Why is that? Additionally, Rocka in the Breakout game (not sure if canon, sorry if not) kills all of Black Phantom's henchmen. These henchmen were never released in set form, and Rocka seemingly tells no one about them.
5) HF might be selling off their weapons to villains on the side. Remember 1.0 Furno's bike? We got a nice Bohrok faceplate re-color out of it. Then remember how Speeda Demon was basically riding it's repaint in Breakout? Where do you think he got it? If you said "He stole it, duh" ask yourself why HF never reported the theft. Answer: Speeda Demon didn't steal it. Back to square 1.