I'm sorry to hear about the kids' falls.
I don't have your trailer and I'm not sure of your bungee/Velcro ystem, so I'll just describe the system we have on our Shamrock/Roo. We've never lost a kid out the side or end on our trips.
Our current trailer is a Shamrock 233S. There are five snaps across the end of each bunk. The sides of each bunk are closed by bungee cords connecting one side to the other. There is a "child guard" flap that goes under the mattress and attaches with Velcro to the top of the bunk wood on both sides, although I usually forget to do that.
Bottom line is that there is no way that anyone is going to fall out the sides or ends with this setup.
You might consider reinforcing the Velcro with some product like this
Also, do you think there is too much slack in your canvas?