I've been playing with layers in the most basic way, camera on tripod, object on table - move object - retake shot etc.
Then I've been going to Photoshop>Automate>Photomerge>Browse>Add files>Untick blend images together. This method automates the process of adding the images in a layer stack and works great in my test images.
However, yesterday I shot a half dozen images of a jet fighter moving across the frame except this time when I do the same process Photoshop tries to make a panorama.
Well, that's what Photomerge is supposted to do, merging. I'm not sure as to what your goal is but you may want to try 'Files|Scripts|Load Files into Stack' instead.