This alert is confusing because you're right, you're not manually changing anything. The error is a message from Meta to your server, saying: "Hey, when a user clicks on your ad and makes a purchase, the unique click ID (fbclid) I sent you is not being passed back to me correctly by your server-side tracking."
Here's the breakdown:
The fbclid: When someone clicks your ad, Meta adds a unique identifier (fbclid) to the end of your website's URL. Your Meta Pixel is supposed to grab this and store it in a browser cookie called _fbc.
The Server's Job: When a crucial event like a Purchase happens, your server-side tracking (Meta's Conversions API, which Shopify's native integration uses) is supposed to send that exact, unedited fbclid value back to Meta.
The Problem: For a small number of your purchases (the 2% you mentioned), the server is failing at this. It's either sending a corrupted, truncated, or lowercase version of the fbclid, or it's not sending it at all.
This usually happens not because of a manual code error, but because of a minor technical hiccup in the way your server (in this case, Shopify's backend) handles and passes that data for some of your customers.