This error means a stock change on Etsy did not reach Shopify for one variation. That variation's SKU is also used by another variation, so Shuttle could not tell which Shopify variant it belongs to. The other variations in the product were still updated, unless your sync history shows a different error for them.
Why it happens
Shuttle pairs each Etsy variation with a Shopify variant that has the same SKU. If a SKU is used more than once, Shuttle does not pair it. Check for:
Two or more variations in the Etsy listing that use the same SKU.
Two or more variants in the matched Shopify product that use that SKU.
How to fix it
In Shuttle, open Stock Syncer, go to Quantity Updates and choose Errors & Warnings. Find the product that shows this error.
In Etsy, open the listing and check the SKU of each variation. Give every variation its own SKU.
In Shopify, open the matched product and check its variants. Each SKU should appear on one variant only, and it should be the same SKU as the Etsy variation it belongs to.
Save your changes. The next time the product updates, Shuttle pairs the variations by SKU again and stock syncs as usual.
Sharing a SKU on purpose?
If several Shopify variants share one SKU on purpose, see Syncing Duplicate SKUs Within the Same Product. That setting (Settings → Stock Syncer → General, under Duplicate SKUs) gives those Shopify variants the same stock level. It only works when the shared SKU is in Shopify, not in the Etsy listing. The Etsy variation still has no match of its own, so you will see the No Matching Shopify Variation Found error for it instead. Giving every variation its own SKU is the only full fix.
Still seeing it?
If every variation has its own SKU on both Etsy and Shopify and new stock changes still show this error, contact Shuttle support. Include the product name and the SKU.