Weird problem happening with custom taxonmy when creating/updating posts

This is a bug in wordpress core when there is a mismatch between the type of taxonomy the taxonomy and the metabox type you use to display it. you must use hierarchical display for hierarchical taxonomy, and “tag like” display for non hierarchical taxonomies.
If you have to have a mix you will need to write your own metabox. This bug is very old, and it doesn’t seem like it will be solved any time soon.

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