Steps to reproduce:

1. Create new taxonomy "categories", follow the steps from the documentation (https://doc.ibexa.co/en/4.1/guide/taxonomy/taxonomy/#__toc).
2. Create some tags under the default "tags" tree and some tags under the "categories" tree.
3. Add two taxonomy entries to Article Content Type ("tags" and "categories").
4. Create Article Content Type and try to select root for both taxonomy fields.

Result:
The tree that is loaded in both fields is the tree of "tags" taxonomy.

Expected result:
You should see "categories" tree when selecting parent of second taxonomy field.

Note:
In both cases the AJAX request is as follows: localhost/admin/taxonomy/tags/tree/1 but in second case it should be localhost/admin/taxonomy/categories/tree/1.

As of now vendor/ibexa/taxonomy/src/lib/Event/Subscriber/ConfigureMainMenuSubscriber.php is broken so creating a second taxonomy using UI should be done using a workaround:

1. disable the menu generation in the mentioned file.
2. create a "root" category entry.
3. enable menu.