It would have to do with the repeater field name. For example if you have a repeater field with field names like
- repeater_fields
- text_field_1
- text_field_2
and another repeater field like
- repeater_fields
- text_field_3
- text_field_4
There’s a chance that this could confuse ACF.
Other than the reasons I’ve covered there’s no reason that this should not be working. The only thing left is some action or filter function that’s interfering with ACF operation.