I had this exact same issue!
Not sure if this helps, but I was using the Taxonomy Field add-on by Brian Zoetewey previously, and disabled this when ACF gained this functionality. However the bug still remained. Today I removed the Taxonomy Field Add-On completely, and upgraded ACF to the latest version, and this functionality started working perfectly!! Such a winning feature.
One question though – it would be awesome if you could present the option to hide a CPT meta box from a edit screen? As it is, you can only hide default cateogies or tags. However, if we are using this feature, there is a good chance we are using a custom taxonomy that we want to hide – as we are replacing the default taxonomy meta box with our shiny new ACF meta box.
I know you can ‘hide’ this from the options panel up top, but a sneaky client might find this, and then have the ability to choose multiple tickboxes again 🙂 Be good to hide it permanetly if possible.
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