If you have multiple shops using the same Algolia application, and see overlapping or duplicate products across them, this might mean the shops are sharing the same index.
Please ensure that different shops have different index prefixes. You can update prefixes by going to the Settings tab of the Algolia plugin.
Please note that updating the prefix will trigger a full reindex of your products, which may take some time.
You can also review "Can I use a single Algolia account for several Shopify stores?" Support article.