It is most likely due to the fact that when you manually input the information, there are some slips that have not been added yet, but when you auto-fill with the CRA, you get a full entry of all your slips which gives you a better calculation of the return. I will advise that you a) choose to use the auto-fill and enter the remaining information or b) choose to do it manually. If you use both methods, you will likely end up with errors or miscalculations.
Review the link provided below to assist with what slips are brought over into TurboTax and whatever is not on this list is what you will enter manually:
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