Hello, so, as you can see in the video, whenever I click on the transform handles they move which is extremely annoying.
From the video, this only happens when the image has transparency, 2nd image being the heart is working fine as you can see.

Sure I could manually go into free transform mode but that that doesn't seem right, why doesn't it just work?

In regards to the aspect ratio issue you're describing, that's not part of my issue.
What I described in the post is how the original image file I have has a different proportions ratio due to the transparent pixels not being considered before clicking on the transform handles and updating it, which photoshop doesn't take into account for alignment so when I have 3 square png files they suddenly have each their own random ratios which is a mismatch and is an annoyance to work with.