The select2(‘data’) method was called on an element that is not using Select2

This is an issue for me as well. Running WP v4.9.4, ACF Pro v5.6.8, and Yoast v6.3.

Overall this is a great plugin! The hard work put in by the developer to build this plugin is much appreciated. Looking forward to the next update for a fix.

While we wait for an update, change this

line 693 on yoast-acf-analysis.js
terms = _.pluck(
  field.$el.find('.acf-taxonomy-field[data-type="multi_select"] ' + select2Target )
    .select2('data')
  , 'text'
);

to this

terms = _.pluck(
  field.$el.find('.acf-taxonomy-field[data-type="multi_select"] ' + select2Target )
    .select2()
    .select2('data')
  , 'text'
);