Photoshop’s automated alignment tools are quite impressive; however, they aren’t perfect. When auto-alignment fails to work the way you need it to, sometimes it just means you have to do the work yourself.
In this video from Ian Norman, he walks us through the process of processing Milky Way astrophotography images by manually aligning them in Photoshop in order to reduce noise and bring out more detail in the images.
If you are looking to improve your astrophotography images, Ian’s videos are worth a watch. Even if you are doing other types of image stacking, you can probably learn a thing or two from Ian’s workflow.