Most travel agents assume their clients don't really know or understand the intricacies of airline fare classes. Rather than ask if you would prefer to pay more to retain your current fare class (and go through a lnog explanation of why), it looks like they took the path of least resistance and re-booked you in a lower fare class, which avoided you having to pay an upcharge.

If the miles or upgradeability are important to you, yes you should complain long and loud to the travel agent and have them fix it - as well as making a note in your file for future that fare class matters to you.