For some reason when you remove an insignia, it will create a new stack, taking up an inventory slot even if you have that same item in your inventory. Happened with unbound blue barbed insignia of aggression, but happens with pretty much every insignia.
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What I tried were all unbound insignia (blue Enlightened Insignia of Prosperity).
Based on your description, I interpreted your insignia issue was just it did not stack automatically when it was removed from the mount and you could stack them together yourself manually. Was my assumption incorrect?