Not really, especially the last two. The first one is in the 'humans fucked up' category which is unrelated most of the time. The other two are mostly the same from the description.
What you must understand is that in the first case, humans are the murderous eldritch abominations. You could argue that the third case is that 'aliens fucked up' seeing as it is comparable to how greenhouse emissions fuck up other lifeforms on earth. The second case is the only one where incompatible perspectives was even a factor, since in Mission 1 the alien inscriptions could actually be interpreted into a form understandable by humans and in Mission 8 it was impossible to really do anything about the microbes that just happened to kill people by sheer chance. There was actually intent in Mission 3, an intent to escape, even when people died, likely due to it not understanding human mortality.
I would also like to point out that something as drastic as killing is what makes them noticeable in the first place. It is far easier to interact incorrectly than correctly, hence eldritch entities that interact are more likely to do so in a manner that proves unfavorable to humans. That being said, it is also quite likely for no interaction to happen. For all we know, everyone could be infected with eighty different earworms, surrounded by a hundred different kinds of genetically engineered alien microbes and pass by five alien life support systems every day. But as long as none of them interact in a way humans perceive to be meaningful, they would fail to even acknowledge their existence.
Supposed the Mission 3 earworm did indeed manage to peacefully influence the researchers to release it back. What would have happened? Nothing. They probably wouldn't have even noticed it. No one would have died and the HMRC would have never been sent in. We would have never even heard about it. What if the Mission 8 microbes didn't coincidentally induce murderboners? Well, they would have found weird structures, found fuck all and just sealed it off before moving on with their lives. The HMRC would have never been sent in. Suppose in Mission 1, the HMRC deciphered those inscriptions correctly, realized that the life support systems would be shut down if they performed that action and decided not to. They could have done nothing for those crystals and would have just left them there for until it reached a certain criteria centuries down the line for them to be released. The crystals may have not even noticed the existence of humans.
My point is, when they interact, it is more likely for them to do so in a negative manner, if they do not interact, they won't get noticed. It is just like how we know about dictators and mass murderers but not people who lived out their lives peacefully and died in anonymity. I would not refer to it as a cliche as much as just a mere statistical phenomena.