I kindly ask you to run this test: Manually update the WPML Multilingual CMS and String Translation plugins to version 4.6.0 and then update to v4.6.9, then apply the workaround described in the errata page and check if the issue disappeared.
I manually updated to 4.6.0 and the issue appeared at this point.
I then updated to 4.6.9 and the issue was still there.
I then updated one of the clone fields to be group and it seemed to fix the issue for all.
I reverted the change to group and the page still seems to work fine so it may be that saving the field group sorts the issue out.
I'll try on production and see if that works there as well.