Hi Ahmed,
That’s a great question and I wrote an extensive answer, but then my answer was lost, because I was mistaken for a bot😉
Let’s try this again. I’ve never seen anybody so brave as to use Extrude Manifold together with a Bevel Modifier.
The truth is, that Extrude Manifold is a bit of a hack and can be somewhat buggy at times. I don’t know how it works exactly and why it seems to break the Bevel Modifier (it doesn’t appear to create double Vertices), but as mentioned above, disabling Clamp Overlap should fix it.
