As long as there are no other violations, this shouldn't be an issue. Yes, prior to Make Ready the shooter should have staged mags as long as they didn't have to go into the same compartment as the firearm. Personally I would have mentioned to the shooter (after the CoF) that it would be better to stage prior to loading the chamber. Reduces the risk of bad things happening.
I actually did this myself this past weekend. After Make Ready I was loaded and at low-ready but there was a timer issue. So I put my RFPO down on my case, pointing downrange, to free my hands to fix the issue. After correcting the issue I picked up the pistol and got in position again.
Now, had I AD'd when picking back up, then that's on me.