You say, "backing them up on iCloud," but iCloud isn't a backup service. iCloud Photos is a synchronization service. When you engage iCloud Photos on a device, then the Library on that device is kept just the same as the iCloud Photos Library. So, for instance, if you take a picture with your iPhone, it is added to the iPhone's Photos Library, copied to iCloud Photos Library, and then copied to the Photos Library on each of the other devices that you have connected. If you delete a picture on your Mac, then that picture is deleted at iCloud and on all the other devices.
So, if I were you, I'd turn off iCloud Photos, and then I'd go to iCloud.com to see what's there. Both on your phone and at iCloud,.com, be sure to check Recently Deleted to see if your missing pictures are there.
You should look at the available storage on both you phone at Settings>General> Storage, and at iCloud.com to see if you have at least 10% of your storage free.
Let us know how it goes…