Funny enough, I did the same. I uploaded the pictures I took first, then after a while, I uploaded the scans.The first scan I uploaded was just a picture I took from my camera but then next time, I properly scanned my diploma. So even if they reject the first scan, hopefully, they will accept the second one.
I do not understand how it could be a reason for rejection. Technically we are not obliget to upload anything, at least in my case. My documents requrements are original transcript, a phisical copy of certificat and translation which I sent to WES. So uploades that I made are just to support them and to safe some time for their team.