Severe headache, blurry vision, stiff neck. ct scan normal. er doc felt confident. could a ct scan have missed a cavernous sinus thrombosis?

Unlikely : Clinical suspicion comes first ,then confirmation or ruling it out by imaging studies comes second. There are signs for cavernous sinus thrombosis that you don't have and that's why the ER doctor felt confident not to go this route. These days, or even earlier, cases are very rare, and your symptoms are still common to other common problems, have a second opinion if you wish, good luck

It depends: on the technical parameters of the scan. If it was performed without IV contrast or performed as a "routine" head CT not specifically tailored to look for cavernous sinus thrombosis, yes. CST is a clinical diagnosis, so if there was no clinical suspicion, there would be no reason to tailor the CT scan.