When I change to a different scene by clicking on it in the scene area and immediately click an object in the new scenes' object tree and delete it by pressing <del>, it will indeed be deleted (this is OK). But also a dialogue pops up whether I really want to delete this scene (which is not intended - I'm glad Sencha asks since that is not reversible).
But: If I click into the scene after switching to it (even click besides the canvas area in the grey background) and then select the object in the object tree, everything works as expected: only the object is deleted.
For me it looks like that selecting an object in the object tree of another scene doesn't also de-select the old scene (it is not clear which scene Sencha wants to delete). But by clicking into the new scene before deleting the object, the old one gets de-selected and everything works fine.