After some time with WPML support and with some debugging/digging in the theme’s core files, I found where the breadcrumb was created. I pointed this out in the support and to also add the taxonomy on pages also in their filtered queries.
I was using default WordPress queries and I was aware that taxonomies on pages are not the default use in WordPress. Also, there was a conflict with WPML and the table “taxonomy” restructure.
If anyone else ever comes across this problem or similar, you will have to update your WPML version to 4.4.4 and above.
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