I should note that it's commonplace for an agent/agency to add its own email to PNRs. I add my email, for multiple valid/useful reasons, to all PNRs that I put together... alongside the passenger's email.
The passenger's email goes in the normal email field with a name association, and also can go in a SSR CTCE for operational contact purposes.
What's not acceptable is to not add the passenger's email and/or not correctly associate it with the passenger's name when there are multiple emails. It should be clear looking at the PNR which email belongs to the passenger (vs that of the agency/agent).