Per this KB article: https://kb.blackbaud.com/articles/Article/101242 a parent list will also include non-parents in the results such as aunts, uncles, etc. even if the corresponding checkbox is not checked which make absolutely no sense...at least to me and my coworkers. It also states that it looks at who was entered first into the database so if an aunt was entered first, she will be pulled before the child's parent(s).
The resolution in that article wasn't working for me and support tech had to find another way to get the results that I needed..but even that isn't working for some of our more complicated lists. It seems that logic would dictate that if a student has a relationship that is an aunt/uncle, grandparent, etc then those people should NOT be included in the results when you are choosing Parent as a filter.