Photos I markup on iPad appear on iPhone via iCloud, but don't download to iPhoto

iPhoto is downloading the unmodified originals from the iPhone, not the edited versions, unless you duplicate the marked-up version of your photo as a new photo on your iPhone. Air-droping the current version will transfer the edited version and not the original.

But even after saving a new copy to the camera roll iPhoto may not be able to handle the mark-up version, because the last iPhoto compatibility update (iPhoto 9.6.1) has been released for OS X 10.10.3, long before Mark-Up has been introduced by Apple.

You could import the new photos with Image Capture to a folder on your Mac, then import them from the folder to iPhoto and see what you get and if there is a format problem.

xristinaathina, you are aware, that your current system version is the last version where you can run iPhoto at all, right? It is high time to prepare for a migration from iPhoto to some other program to handle your photos. The problem ist, that the newer system versions will no longer be able to run iPhoto, and sooner or later you will have to replace your current Mac, and any new Mac will come with a system version that does not support iPhoto. The migration should be done, while you still have a Mac that can run iPhoto and also can run the successor application you want to use. Mojave is the last opportunity for an easy migration. If you wait until you are stuck with a system version that does no longer support iPhoto, it will be impossible to run the Photo Library upgrader tool, it will be impossible to compare the iPhoto Library to the migrated library and fix issues, like missing metadata or incomplete smart albums, it will be impossible to convert videos and photos in a legacy format in your iPhoto Library to a format that will work on the new system version. In short, it will be a lot more work and you may may lose photos if you wait until it is too late.

Try going to iCloud.com using a computer browser to see if the items are there and whether they are from the device or the computer. That should show whether the device or the computer isn't syncing. If the computer, try going to System Preferences/iCloud (Apple ID if you are using Catalina or later) and stop syncing. Wait a couple of minutes, then recheck syncing. If the device, go to Settings/Your Name/iCloud and do the above. As a last resort, you can also try signing out of iCloud and then sign in again.