This is not a bug. It is a (perhaps slightly unfortunate) consequence of Blender's selection propagation. When you're in Vertex mode, you have a fully contiguous selection: edges between the circles are also selected. Since it is contiguous, there's only one "origin", therefore the selection is transformed as a whole. When you switch from Vertex to Edge mode, that edge selection is preserved, so you again have contiguous selection. It is when you switch to Face mode the selection becomes disjoint, and each selected "island" has its own "individual origin" for transform.

@Stanislav Blinov (radcapricorn) But it worked in previous versions though! if you bevel a row of vertices and scale them on their "individual origin" in 2.80 or 2.81 works, in the master branch even when extruding includes that contiguous edge where before it wasn't that case.

Here is a 2.81 Demo.

That which you show in that example, I believe, is actually a bug. When you bevel the vertices like this, the selection readout at the bottom right will state that 20 edges are selected, where in fact there are (should be) 24. If, after such bevel, you switch to edge mode and back to vertex mode, then all 24 edges will be selected, and the behavior would revert to transforming the whole selection.

I believe this behavior is related to one of these two commits by @Campbell Barton (campbellbarton):

1. rB133f6a9812609feda64418ee0c8f318f28e8d8db
2. rBf164ea6eaae541c76a8589837796d81df143c9ca

I'm traveling right now but when I get back to my computer I can look at it. Thanks for letting me know. I agree it doesn't exactly look like a bug.

While the old way may indeed have accidental "benefits", tools really, really should not create invalid selection state. https://docs.blender.org/api/current/bmesh.html#keeping-a-correct-state

In T73771#871952, @Hans Goudey (HooglyBoogly) wrote:

This isn't a bug, and it's actually a bug fix that caused this change. There shouldn't be "individual origins" because all of the vertices are connected by at most one edge.

The technique you brought up still works, just use a different bevel offset to change the size of the holes rather than scaling them. That said, the profile value of 0.1 doesn't create a circle, 0.088 is closer, but the way bevel is coded means you shouldn't rely on the profile to be perfectly circular.

Thanks for the report anyway.

Thanks, i guess the issue goes back to 2.7x versions or even before.
I didn't know that it was a bug to be honest, i thought this is how it always worked because how Blender handles meshes differently from what i used to see in the other apps, but since the new changes fixe a long time bug then no problem, we can use other ways to get the same result.