Sunil, this is an issue when you complete the chart before the MA charts on the vaccines/injections. I agree the solution would be to turn off auto add, but when I went to look for where I thought that feature was, I did not find it. That would be a reasonable answer to that problem.
The other problem, that Julia brought up, is incorrect CPT's. I, and I suspect AC, know about the influenza vaccines. I am not aware of any other ones that are not correct.