I'm not sure how you could have gotten an "extra" one in the first place. It's only available once, as a quest reward for one of the main scenario quests. You should have only gotten one, and when used, it would disappear as an item but appear in your minion list. Some weird bug must have happened for you to have both the summonable Wind-up Cid in your minion list while also still having it as an item.

Did you get the quest rewards from a jump potion? Maybe that's bugged.