Shuttle did not update this variant's stock in Shopify. Its Shopify stock is below zero, its Etsy stock is zero, and your settings tell Shuttle to update negative stock only when Etsy has stock.
Why it happens
Your negative stock setting. Negative stock handling is set to "Update only when Etsy stock is positive". With this choice, Shuttle changes a variant with negative Shopify stock only when Etsy stock goes above zero, for example after you restock.
The variant's Shopify stock is below zero. Check the variant's stock in Shopify at the location Shuttle uses. If you use the combined quantity across all locations, Shuttle checks the total.
The Etsy listing has zero stock for that variation.
This is a warning, not an error. Shuttle is doing what you set it to do.
How to fix it
If you want this behaviour, you do not need to do anything. Once the Etsy stock goes above zero, Shuttle updates Shopify as normal.
To have Shuttle update these variants every time:
In Shuttle, go to Settings > Stock Syncer > Etsy → Shopify.
Find the Negative stock section.
Under Negative stock handling, choose "Update variations with negative stock normally".
Click Save.
You can also fix the variant's stock in Shopify so it is zero or more. The next update from Etsy will then go through.
Still seeing it?
You may still see this warning on new updates after saving "Update variations with negative stock normally", or when the variant's Shopify stock is zero or more. If so, contact support and tell us which product it is.
If the variant is set to keep selling when out of stock in Shopify, you will see a different warning. See Negative Shopify Stock with Backorders.