Split by Features Tool creating holes in polygon dataset

[bw0093]

I'm having trouble with the Split by Features tool in ArcGIS Pro. When I use my impervious polygon data to split the target features (also polygons), it creates holes in my dataset. Has anyone run into this before and/or know how to troubleshoot it? I ran the Check/Repair Geometry on both datasets and those appear to be clean now. I've also checked the domains, as that seems to be another source of error for others, but the only one I've seen is in my Input feature and the Split policy is set to duplicate. There are no definition queries on either dataset as well. 

Any help with this would  be much appreciated!! 🙏