I will try to explain the exact issue I have had today.
2 sisters ....1 sister (Eleanor my gg.grandother) married a David Oliver (my gg.grandfather). Today I found the other sister married a Micheal Oliver (no relation to David). I added this new person by going to the correct sister (Elizabeth) and clicking the add spouse and entered his details.
When navigating up through the ancestors to Eleanor & Davids child it shows the parents as Elizabeth and Michael. However if I navigate from the top down through the descendants it shows the correct parents. However, if I hen click on the child it then reverts back to the wrong parents. I have checked the parents by right click and choosing parents it shows the correct parents.
Let me know if you need any more info!