Illustrator on a Mac also currently has a Layers/Tool bug too. If the layers and tools are just arbitrarily vanishing, turn on or turn off the Application Frame. You might also try updating to the latest Apple OS (or the latest update to the version you are running.)
I am using windows OS and I tried looking for Application Frame from the windows down drop menu to turn it on or off.
I don’t see one there.
Getting back to you first response.
What i mean by clearing the art board.
With the selection tool I high light the image and press the delete key and my image is cleared off the art board along with the new layer of the image in the layers panel.
When you create an object, Illustrator adds a sublayer for the shape on your current active layer. It does that for every shape and object. Delete the object and it deletes the sublayer. Working as designed.
You can create a sublayer using the menu in the upper right of the layers palette. This is basically a new layer. If you create an object on this active sublayer, Illustrator will create yet another sublayer with the shape on it. Working as designed.
Current version of Illutrator has Application frame in Window Menu here: