This is purely the fault of your TA. I switched TAs several times and finally found one that is really good. I never have these problems any more, and have been with this TA for 6 years now and over 300 tickets issued by her.

In the end of the day, the airlines and their computers suck and a good TA knows how to check, double check and tripple check. Then, if there is an error, a good TA can call the airlines and have them waive change fees.

Get a new TA!