Applying join to mesh I'm little bit lost.
I did all of those steps in this tutorial but if I'm trying to join sphere with mesh it outputs weird shapes:



I want to join them to create animation later.
These weird shapes are likely due to Wireframe modifier on the "net" object. When you join them Wireframe modifier applies to spheres too. If you are not going to change settings on Wireframe modifier later, then you can apply it before joining with spheres.