Too long, didn’t read: So the causes of vibe are a unique combination of many things. Some is due to suboptimal building materials. Some from poorly calibrated or operated CNC machines. Some from poor assembly. And some is from “artisan anodize marks” 
I kid, I kid.
Long winded version:
Vibe - everyone’s favorite discussion topic! Most people are simply going to tell you to ignore it and just “enjoy” the yoyo as is. But that advice ignores your question.
There’s a big long discussion post about it worth a read.
But this topic is super subjective, so here’s my “hot take”…
In order to have a “vibe free” yoyo (or any spinning object really), two basic things are required. Weight must be uniformly distributed (or adequately counter balanced) around a rotational axis and both yoyo halves and the bearing must all be on “parallel planes”. When either one of the 2 things are off you will experience “vibe”. It’s worth noting there’s really no agreed upon standard defintion of vibe as everyone’s perception seems to differ so I can only go with my own interpretation.
Weight imbalance will generally be described as “pulsing” vibe. Non parallel planes will generally be described as “fingernail” vibe (and more easily seen as a wobble). But it’s not a case of either/or; realistically, you will probably have some combination of the two thus giving every yoyo a unique feel.
Equal weight distribution generally is not an issue with modern CNC’d metal yoyos because metal is typically extremely uniform in density and CNC machines (if calibrated and operated correctly) are extremely accurate. Now, if you “ding” a yoyo and consequently redistribute mass that’s a different situation.
But I have found the cause of most “vibe” to be related to the second issue about stuff not being on “parallel planes”.
Ideally your yoyo should look like this: |-| Two yoyo halves meeting the bearing and forming a perfect ‘H’ shape. However what often happens is the halves meet the side of the bearing at ever so slightly an angle. A few exagerrated examples: |-\ or /-/ or /-\. Please note I’m trying to illustrate the bearing being the thing not in parallel here not the halves themselves but ascii art is limited. Several things can cause this including (but not limited to): not screwing the yoyo together tight enough for the bearing to be forced to sit flush in the bearing seat, gunk/debris in the bearing seat preventing it from sitting flush, bearing seat post being too large for the bearing’s inner diameter preventing it from sitting flush.
If the bearing and at least one yoyo half meet at any angle greater then 0 degrees you will experience some fingernail vibe. This is because the shape of the yoyo is no longer symmetrical as it spins. As it spins, part of the shape extends out farther and touches your fingernail, |-/
. As it rotates more the shape doesn’t extend as far and does not touch your finger |-\. If a yoyo spins at say 5,000 rpm (just a guess) then it repeatly is coming into and out of contact with your fingernail. This type of vibe will usually get more pronounced as the diameter of the yoyo increases or the angle increases depending on where you are checking for fingernail vibe – like near the axle versus the rims.
“Tuning” yoyos (flipping the axle and other voodoo nonsense) is largely a myth except it forces you to do one thing over and over, disassemble and reassemble the yoyo. This basically just increases the likelihood the planes will be brought closer to parallel because you’ve done something in the dis/re-assembly process to make the bearing sit more flush. As an extreme example, in another post I described how I experimented and ultimately removed the vibe in a b-grade yoyo by shaving down the bearing posts with a pair of pliers until the bearing sat flush. Crude but effective.
Anyway, where was I? Right, artisan anodize marks…