Now the documents has the ACF field which is set to "same fields across languages" so that all fields are copied and WPML manages automatically.
It has one file file where admin and editors can upload the document. Now the issue is we have document in all 4 languages we are using so even if we use auto translate we want to be able to upload the 4 different files in different languages. like the english content should have english version and french should have french one.
The warning is shown because you have set different fields for the translation of field groups.
You can continue translating the pages/contents manually as you did which you said solved the issue and ignore that warning/message.
I recommend you also test translating the contents and updating/editing it to make sure and confirm the issue is resolved completely and there are no other related issues.