I find this aspect of a good creepypasta strangely rarely brought up. Anyway, the "Something Not Quite Right" is a point in most creepypastas where you realize that, as the name suggests, something isn't quite right here.
The first example that comes to mind for me is in "A Game of Flashlight Tag" When the protagonist gets a flashlight shined into his face during the early part of the story there's something odd. The person holding the flashlight is unresponsive to practically everything. Then, he starts walking towards the protagonist, and runs when the protagonist runs. It's at that point where we don't feel something is off about this guy - we know it.
Another example is "To-Do List", a pasta that is unfortunately not on this wiki. Creepsmcpasta did a video on, so you could check it out on his Youtube Channel. Anyway, the feeling of something off starts when Laura begins reading scary stories and writes peculiar and disturbing things on the titular to-do list.
The strength of utilizing a "Something Not Quite Right" is that the audience knows something bad is going on, but they can't put their finger on what. They know something bad is going on behind the background, they just don't know what. It also intrigues the reader to continue because of natural curiosity. Along with all of that, it adds to the general suspense of everything.
Now, how can you write this effectively? Simple. Have certain characters who are involved with this act shifty and/or unnaturally is one way. Let's say the protagonist walks into a town full of people who always seem to be smiling. However, when the protagonist goes for gas one morning, he overhears someone grumbling and complaining about their job. He sees through the window the boss (someone who actually is smiling) gesturing for the worker to follow him. Then the worker looks terrified.
The protagonist goes back to putting gas in his car because there's nothing too strange about that... only to never hear of the guy again. In fact, no one even acknowledges him ever existing. This process rinses and repeats a couple more times with everybody who complains mysteriously disappearing and never being mentioned again.
There is definitely something going on here now. This isn't just one person vanishing into thin air, but multiple people, all doing similar or the exact same things. Something suspicious is going on here.
What to Avoid
For one: Don't come up with an explanation at last second. You could have an amazing pasta, with everybody at your heels expecting a powerful ending. Then you suddenly reveal that the townspeople were pranking this one guy no matter how ridiculous it sounds.
For two: Don't drag it on longer than necessary. Going back to "A Game of Flashlight Tag" the whole scene of the protagonist looking at the person shining a light in his face lasts exactly how long it needs to. It allows us to get unnerved by the presence of the mysterious man all while not dragging on so long that the entire pasta is just this, then a running scene afterwards.
Finally: Don't force it onto your reader. In To-Do List we aren't being constantly told "Hey, listen! Be weirded out by what Laura's writing on the board because it will be relevant later!" Manipulate your reader into feeling like that's the case. Don't have characters continuously exclaim how off-putting things are.
A more specific example for those who need it:
Wow, things were really weird, huh? I mean, that one guy just vanishes into air. It's getting kinda fishy. It wasn't even just a one-time incident - it's been happening a lot! Isn't that just so... so suspicious? I think something else is going on here!
If I was told that shorten that, I would simply write: "Hey audience, something's terribly wrong here!" This especially goes for when somebody does it every other paragraph of saying how peculiar things are.
-Have unusual things go on in the background. -Don't force your reader to think things are wrong, but let them come to that conclusion instead. -Don't drag things on. -Don't have a horrible ending. -With great power comes great responsibility.