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When having Bootstrap theme (or it's subtheme) as your default one, try setting the Administration theme to "Default" (i.e. the same bootstrap one)..
>> At /admin/appearance you won't have the "Administration theme" form at the bottom of the page anymore!
So the only way to switch back from the UI is to set another theme as the default one, then changing the Administration theme setting, and resetting your bootstrap based theme as Default.
Try also to make a VBO view and you won't have the operations form at the top of the View, it doesn't matter the permissions or the path you set..
Yes you can see the checkboxes in the Views content rows, but you don't get the select list and the button to execute the operations before the View.
I am quite sure there are other forms which magically disappear when using Bootstrap theme. Will update this list..
UPDATE: probably is fieldsets not rendering, as in all cases above the hidden forms where fieldsets.
This was clear when I also found out the problem adding a node with a multivalued image upload field.
When using the admin theme it would always show.
When using a bootstrap theme it would only show when the image field is set on single value. When using unlimited values, the field is shown in a fieldset, and disappears from the form if the theme is a bootstrap one.