One thing to consider...the travel agent might have made an improper booking (either deliberately or by mistake) by somehow pricing something they should not be able to.

It probably won't affect your trip, but the TA is likely to receive a debit memo (chargeback) from CO for the fare difference if they constructed something that was not bookable. A travel agent can pretty much book and ticket anything they want - if it's not legitimate, they will just get charged back for the fare difference.