I'm not sure I follow...how much time between your TA booking and checking online? Perhaps additional seats were released in lower fare classes, maybe you were buying from a consolidator, maybe your travel agent listened to your needs and sensibly got you a fare which allows changes which the online source doesn't, etc etc. There are many reasons.

Don't compare apples and potatoes, the underlying tickets are likely to have different characteristics. Don't forget that, until ca 24 hours before travel, the agent owns the ticket, meaning that any changes need to be made through them. A live human is a lot easier to get in touch with to sort out a problem (schedule change, for example) than a OTA call centre that has little interest in helping you.