Nothing that caused a significant hindrance.
It took me a while to get that evolution can kill people even without depleting their energy because (I assume) it lowers their underlying stats, which you can't see until you get to Brain Probe 3. But there are plenty of warnings about that.
Didn't grasp straight away that evolving a better biomineral doesn't upgrade your existing formation(s).
It also took a few plays to realise how to get into the sewers. At first you don't even know it's a possibilty, whereas in later playthroughs I would pretty much try to head down there the second I evolved brain probe. Which, again, isn't necessarily a bad thing - a lot of the fun for me was in discovery and "emergent gameplay" - figuring out little things like storing weapons and smartphones in the habitats, or going after a specific person by letting your current host die in the sewers then (hopefully) riding a dog to hunt for the right human, so you don't have to leave any bodies behind.
Maybe it'd be possible in future iterations to add challenges that can be solved with combat, but have other possible solutions as well. For example, objectives like the ship could be guarded. To get past, you could just kill or invade a guard... but it might also be possible to walk in if you're camouflaged and your host has security clearance. Each has their own potential risks, etc.