I have seen this on occasion. It shouldn't happen, but it usually has to do with the dimensions of the new feature and proximity to edges or vertexes in the part. Nothing jumps out in your screen shots, but I'd try tweaking the dims of the feature to see when it causes the trouble, that can lead you to a solution.
I'd also look for other geom checks in the part. My experience is that a geom check that seems to regen how you want still means that Creo is guessing about what should happen and happens to be guessing right. It can lead to odd results like this later down the tree sometimes. Resolve those and you may clear this up.