Claiming the children on either spouse's tax return will not affect the claim for the Canada Child Benefit (CCB). The only way any changes can be made to the CCB is by contacting the CCB section of CRA.
If you prepare your returns separately, TurboTax is assuming that you are the one claiming the children for the benefit and showing this estimate on the summary for information purposes only.
One thing you want to make sure of when preparing spousal returns separately is that you include your spouse's income. Failure to do so will result in you receiving a "spousal tax credit" in error and having to repay this at a later date.