I have been using the Windows iCloud auto photo/video download (iPhone 8) for several years with no problems. Since upgrading to an iPhone 12 Pro on Dec 8th, most of the photos are downloaded at 2048x1536, with a few at 4032x3024. My phone iCloud is set to "Download and Keep Originals" and Transfer to MAC or PC is set to "Automatic". The iCloud web download also has this problem.
If we understand correctly, some of your photos are not downloading at full resolution. You’re in the right place, we’d be glad to assist in seeking a solution.
Please make sure you are following the steps here to download the photos:
Download iCloud photos and videos
"On your Mac or PC
If your photos download as a ZIP archive, learn how to uncompress the folder on your Mac or your PC. "
If you still need assistance, reach out to Apple Support: Get Support