Hi @Blawkyy welcome to the forums!
When upserting catalog objects, you must upsert the entire object, and change whatever you want to change. Anything that you leave out (like the variations), will be removed/deleted from the item. So, it’s most likely not creating another object with the same id, but probably deleting a lot of the object when you update it. For instance, an item will only appear in the Dashboard UI when it has variations, yet your request didn’t include the variations, so it most likely was deleted from the item.
Typically, we suggest calling RetrieveCatalogObject to receive the whole object, and then manipulate the object changing what you need, and pushing the entire object to UpsertCatalogObject. Please let me know if you have any additional questions or concerns, I’m happy to help!