Theres three ways someone can log into a school/organization in FSP for the 1st time.
By the school creating them a profile and sending them an invitation to it (which does not need the Company ID)
The school sends a generic invitation link without a created profile (which does not need the Company ID) and the user will end up in the "waiting for approval" section.
The user makes an FSP account and requests access via entering the Company ID (No action from the school, also ends up in "waiting for approval").
What do I do if they are getting the company ID screen and should not?
Send them a refresh invitation (from their user profile under online access) and have them click the link from their email and from here they likely need to select "login" at the very top.