I fixed the activation errors by deleting the entries in the wp_options table with these option names:
otgs_installer_admin_notices
otgs_installer_recommendations_admin_notices
I used phpMyAdmin to do that.
If you are not sure how to do that then let me know and I will try to help.
Regarding the extra "Toolset WooCommerce" custom field groups, first let me talk about the solution.
You need to run some PHP code to delete the surplus field groups, i.e. this code:
$cfgs = get_posts( [
'post_type' => 'wp-types-group',
'title' => 'Toolset WooCommerce',
'numberposts' => -1
]);
foreach ( $cfgs as $cfg ){
wp_delete_post( $cfg->ID, true );
}
On your staging site I added a code snippet at Toolset > Settings > Custom Code. The snippet does not need to be active (running continuously), it only needs running one time. I have done that, which has deleted the unnecessary field groups.
The field group is generated automatically, for Toolset to be able to work with WooCommerce fields. Toolset runs a query to check if the field group already exists, and if not, it creates a new one.
The problem—with other users—has arisen because some 3rd party code (e.g. from another plugin) modifies our query so that it fails, and therefore the group is recreated. The 3rd party code intends to modify some relevant query, but does not target that query correctly, and ends up changing other unrelated queries.
The challenge is to identify the 3rd party code, which essentially means running tests with other plugins disabled while performing basic actions with WooCommerce like visiting the list of products in the back end.
But on your site you no longer have the Toolset WooCommerce plugin activated, and if you don't use it, the problem should not occur.
