I think I’ve isolated the problem a bit.
I’ve the following field group
When I add it to a flexible content layout field twice using Clone field, the first one is controlling the second too:
I tried adding a field in between to separate them (has worke with similar issues in the past) without much luck. If there are multiple instances of the flexible layout on the same page, the bug is the same in each one.
It doesn’t seem to matter if the clone fields are prefixed or not.