Do you have two marriages entered for this couple, so that on the spouse icon for each of them there is a 2 (or higher number if they've married other people as well)?
Assuming you do, do you have the children linked to the first marriage or the second? The 'right' one is whichever marriage was current at the time of the child's birth.
If you have a child linked to the wrong marriage, put the child in the parent (middle) position in Family View, right-click on that person and then select Unlink > from parents.
Next, right-click on that person again, this time selecting Add > Parents, and navigate to the correct marriage and select it.
Hope this helps. Keep asking questions if you need more help. :-)