"Now I can't select an object by clicking on it or by selecting the layer manually."
What exactly you mean? It was never feature to click on object and select it unless you use Magic Wand but that is also questionable whether you can select every object.
-Selecting layer manually - do you want to ask for Ctrl + click on layers thumbnail? That should select what is on layer, if you have object surrounded with transparency then that can do trick. Is that broken, does not work?