For anyone concerned, manually adding the code to your website, rather than via the native integration solves the problem and its back tracking normally now.
I also spoke to Squarespace's support team about this and they said the following:
You're welcome to let others know that the issue has been flagged with Engineering. That said, the other customers you're speaking with are also welcome to reach out about the issue. This way, the impacted sites can be measured accordingly.
So if you are having a problem, do reach out to them!