I never noticed it before, I guess when I’ve done this I’ve never looked at the ACF admin on the secondary sites because I never planned on editing fields there.
There is one way to solve this, but you’ll need to do it every time you edit a field group. You need to edit the JSON file. The end of the file will look something like this
"active": 1,
"description": ""
"modified": 1558547253
and you need to add a line
"active": 1,
"description": ""
"modified": 1558547253,
"private": true
but like I said, you need to edit the file every time you update it on the main site