iCloud Photo Library syncing

Yes, just accept that anything you wifi to your iPad will also be synced via icloud. Especially if what you send by wifi is in *any* way different (including file date) from the one that gets added to your mac.

Your alternative is to add all the wifi transferred ones to an album so they can easily be deleted later when you sync via iCloud. (I sometimes do the same when I want to share camera images before I get home). Or if the camera imags are shared as jpg via wifi, but added as raw on the mac, you can use a smart album to identify jpg files from that camera and delete them from the smart album.

Do you mean you have put the mac photos on the phone by USB sync, but are using iCloud to transfer from the phone to the Mac?

If so, that is not the way to do it. You should either use iCloud, or USB, but not both.

iCloud will always sync the libraries of devices connected to it. But photos transferred to a phone via USB (synced albums) are not actually stored in the library. So if you use this method then iCloud will still transfer the photos into the library.