Do you mean that you import the compressed PNG files in the Unity Editor, and that you see the above green colorin transparent areas in your scene? If so, then perhaps you have exported your atlas images as Premultiply alpha
(PMA), but your PNG compression tool does not respect PMA at all. Another guess might be that the PNG files are not written with proper alpha channel information. Without having the problematic files at hand, we can't really tell.
Apart from that, if you do not directly download PNG files to your game but first import them in Unity and then create asset bundles or addressables or somthing like that, then Unity will take care of any compression and your initial PNG file compression is only used by the Unity Editor (so it's not used in your game), as I mentioned in the posting above.