I entered an amount of self employed commission from a T4A in the correct place but do I also enter the amount in the T2125 section for my commission income?
That's correct, it should automatically transfer over. (I've attached a picture of where the amount should show up on the T2125.)
Is it possible that you are looking at the wrong T2125? If you go into the summary of the self-employed section, in there is a list of all the business forms created for your return. You should be able to adjust and/or delete any of the business forms.