There are things that can make fields disappear, but, that usually happens when you have many, many fields and is associated with a PHP setting. From what I can see you don’t have nearly enough fields in the group to cause this.
What’s really odd is that it appears the fields are all there, because the field order number is not in sequence and it’s like some of the fields are hidden. When you get this happening try inspecting the source of the page and see if you can find a reason that some of the fields may be hidden.
You could try turning on error reporting and the next time it happens look in your error log to see if any PHP errors occurred. But you’re right, unless you can give me a way to reproduce the error it will be extremely hard to find. https://codex.wordpress.org/Debugging_in_WordPress
