I’ve had this happen on a site in the past, and I don’t know what caused it. In my case I was using a flex field. I copied a field in one layout and then moved it to another layout, after saving the field group the field had moved itself back to the original layout. I believe this was being caused by the parent not being set correctly when moving the field. I never tracked down the cause. I corrected the situation by only creating fields directly in each layout. Added some work, but I needed to get the project done. There was probably something going screwy in the JS for this site.
A repeater could cause the same issue. If you create a field at the top level and then move it into the repeater, if the parent is not set correctly before saving then the field would likely move back to the top level?
On the other hand, if you created the field in the repeater…. well, I don’t know, unless there is something wrong with the parent setting when the field group is submitted for update. It could be that some other script running on the page is interfering with this.
