Shuttle did not update this variation's stock in Shopify. Its Shopify stock is below zero, and your settings tell Shuttle to skip variations with negative stock.
Why it happens
Your negative stock setting is set to ignore. In Settings > Stock Syncer > Etsy → Shopify, the Negative stock section has "Negative stock handling" set to "Ignore all variations with negative stock". The default is "Update variations with negative stock normally", so this option was chosen on purpose at some point.
The variation's Shopify stock is below zero. Shuttle reads the stock at your selected Shopify location. If you have more than one location, open Settings > Products > General and check the Shopify inventory location section. When "My Shopify variations are stocked in a single location" is unchecked and "Quantity source for Etsy updates" is set to "Use combined quantity across all locations", Shuttle checks the total across all your locations instead.
How to fix it
If you want Shuttle to update these variations again:
Go to Settings > Stock Syncer > Etsy → Shopify.
In the Negative stock section, open "Negative stock handling".
Choose "Update variations with negative stock normally" to update them from Etsy again, or "Update only when Etsy stock is positive" to update them only when you restock on Etsy.
Click Save.
One exception: a variation set to continue selling when out of stock in Shopify is still skipped while it is also sold out on Etsy. See Negative Shopify Stock with Backorders.
If you want to keep ignoring negative stock, correct the variation's stock in Shopify so it is zero or higher. Shuttle can then update it again on the next sync.
Still seeing it?
Contact support if the warning keeps appearing after you changed and saved the setting, or after the variation's Shopify stock is back to zero or higher. Tell us the product and the variation name.