It seems that there are pages that can’t detect CSS under common.scss and even initialize.js. What I usually do is to place the code under footer.html or header.html but adding the codes there are very limited compared to creating an enter js script or sass script where you can use variables. Some of the pages were /u/activate-account/{token}, 404 page.
Is this on your local or on a production site? Locally, I see this theme CSS on /u/activate-account/{token} (but only after a refresh), I tried with this: