Hard to tell what caused it. I did a site plan which was just a quick tracing of an existing site plan and then made the mistake of plotting a PDF in perspective instead of parallel projection and the whole thing was off. A slight perspective view might throw things off. Any little object with a positive or negative z value.
I use flatten.lsp in Autocad to flatten all line work most of the time. This is especially useful when you're drawing over a survey with topography that can be thousands of feet above the ground plane. Even a 3D door will do the same when snapping lines. I'm still old school with Autocad using what's basically a modern version of Autocad 15 and 20 years old. Works great.
Non-planar faces in Sketchup can also create a mess.