We recently had a contact unsubscribe from an email that was sent with a transactional send classification. This email did not have an unsubscribe link and having been seeded into the email, I cannot see a way to unsubscribe from these emails.
How could this have happened? Is there any other way for a subscriber to unsubscribe without clicking on a link?
It really all depends on your unsubscribe process. The default Marketing Cloud Profile Center page will unsubscribe the person at an All Subscriber level. This means that all emails sent as "Commercial" Send Classification will not go to this person. However, triggered emails usually should have the "Transactional" Send Classification set, with NO unsubscribe link included in the email(since there is no legal requirement to include an unsubscribe link in a transactional email). So basically, if you set all your other triggered emails to transactional Send Classification, all people will receive them no matter their unsubscribe status.
In my experience, the only way to achieve this globally (and without code) is to use the unsubscribe/resubscribe custom links. It sounds like you are already using this (included with the Installed Package). Even if you resubscribe the contact in Marketing Cloud, it will not share the update with the Email Opt Out field in Salesforce.
Best Answer
Please check this link - it is possible they might have replied: "Unsubscribe" to the email, if you have RMM - reply mail management configured in a certain way.