You cannot have both an ACF taxonomy field that saves/loads value and the standard WP meta box for the taxonomy at the same time. Whichever one is processed last will override the one that is processed first. If you are going to have a taxonomy field to do this then you need to set the metabox callback for your custom taxonomy to false.
Another thing that can cause this is having taxonomy fields is repeaters or flex fields. This will not work with save/load terms for the same reason you can’t have the taxonomy field and the standard WP metabox. Whichever one is process last will override whatever is in the ones that are processed first.
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