Help needed with hook_node_submit in custom module to save data
So now I can answer my own question:

In my module I had $form['container'] defined in the hook_form_alter(), but the actual field $form['container']['main_taxonomy_term'] wasn't defined yet as I was adding it in my callback, so naturally Drupal didn't know about the field when rendering the form. 

I restructured the module, moved the $form['container']['main_taxonomy_term'] = array(...) into the hook_form_alter(), created a new function to get the select options, calling upon it in various circumstances, added some extra checks for the edit node form as the options had to be built from the database values upon first display, but after that use $form_state else it wouldn't refresh the list upon editing the checkbox selection...

Oh well, so i finally managed to get it working without error message.

Maybe this is helpful for anyone, or maybe it isn't at all.