Yeah, there's the possibility of getting counter-hacked when you fail a hack. There's the enemy mucking you up with the smiley virus, which requires you to debug by hacking yourself, or the much more version of them using Destroy on you, which apparently bypasses your reanimators and everything, and goes straight to "nope mission failed".
Blargh I was on the story first mission, having bypassed a monster-infested garage without alerting any of them and stomping through a horde of looters, only to (repeatedly) fail to hack a buncha turrets and get my cybernoggin melted and everything invalidated. Not cool.
...To be fair, it's probably the game's way of telling me "your character only has 17 hacking, stop trying to be a hacker". And it's completely possible to avoid any consequences if you close the hack menu before you fail.
There's also the after-death mutilations thing, permanent penalties to stuff after dying. That kinda sucks. Apparently those are removable after researching... something, but AFAIK it's impossible even with money or stuff otherwise. My first one was because I was rushing trying to get back to the random mission hall, and fell into one of the billion death pits the temple's built over. 240 meters is a long way for my 80% speed-malus'd self :<