Multiple small glitches when beveling complex meshes I have a repeated problem with beveling complex meshes using the respective modifier, even if all what I do is to combine off-the-shelf geometric primitives with off-the-shelf modifiers, without any individual vertex-level manipulations. The effect looks often like that:



I tried to change the bevel modifier's many options, but the effect is that either the bevel is gone completely or the glitches become even larger.

Here is a link to the model 



To work around this problem, I finally replaced the second bevel with a lattice and it even gave some more control on the shape.
The glitches are caused by overlapping vertices. The only solution is proper topology, supporting the bevel.

If we examine the effect of the bevel modifier on your topology, we can see the vertices are badly positioned and the bevel quickly creates overlapping faces.



Position your edges parallel to each other and assert that the edges have a minimum length.
(In your file I had to apply previous modifiers.)



When you enable the Clamp option in the bevel modifier, the bevel modifier will determine how much it can bevel before vertices/edges overlap. However, if there are dense parts in your mesh this value will be very small and result in a tiny amount of bevel. This question shows that a solution would be to split the mesh into different parts, or use bevel weights in that case.



If you model geometry, especially using n-gons, be wary of the spacing of the edges and the topology. If you add a support loop (simply inset and scale), the first bevel modifier will work fine.