I have a lot of duplicate items caused by errors in the Wishlist program and I don't believe them all to be related to variations. Firstly, if you part out and you choose the variation you need. At this point, having verified and submitted, the variations flag should be excluded from any further selection process thus ensuring the integrity of the Wishlists. I'm not entirely convinced that variations is the route cause because I have experienced bizarre Wishlist errors and these I'm sure are a result of the Wishlist program error routine. Sometimes when I'm selecting and deselecting Stores an "Unspecified Error" occurs. At this point does the program reset all it's parameters and update queries or does it blindly bumble on reeking havoc with the Wishlists and Carts.
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Would you be able to give more information about the error you receive? Is this a red error message that appears at the top of the page? Does it only have the words "Unspecified Error" or is there any other information?
With regards to the 7743 Wishlist, I presume the part has since been removed from the Wishlist. It may be pertinent to note the majority of that WishList was created all at once in September, and then another 14 parts were added to that over two days in November so it's possible the part was added to the WishList manually afterwards.