Regular gems sell for twice their value in coins (the amount of coins you can hold caps at 500k though, and UGs give 50 orbs on top).
When any gem is dragged to the sell bag, the prompt shows up. Judging by the way you worded your post, it did actually come up as it was supposed to. In case your son pressed the x instead, the gem would have remained in the inventory (same as when you'd press no). The only ways gems are sold is by tapping yes, or by gems getting auto-sold as you steal others.
If some strange bug truly occurred here, it would be the very first time I'm hearing about it (doesn't mean it's impossible, just implausible).
Unfortunately, I don't think anyone can help getting this gem back.