I often import parts from Mouser (SamacSys). Most of the time they render correctly, but every now and then one of them will show up with the wrong edge on the PCB, like these resistor networks:
This is called “tombstoning”. Sometimes it’s an artifact caused during soldering, for example when one pad heats quicker then the other and there fore the solder on that pad mets faster and pulls the part away.
But in the digital world…
The 3D file and the footprint are two separate files made with different pieces of software, and there are no hard standards of what the “X”, “Y”, and “Z” directions are of a 3D part. So if you add to that 3D parts found on the 'web you get stuff like this. I assume the KLC has rules for orientation of 3D parts, and with footprints and 3D symbols from the official KiCad libraries this should not happen.
But as stuff like this is common, KiCad can rotate the 3D parts.
You click on a footprint to make it active, then press e for edit, and on the 3D settings tab:
you can edit parameters for scale, rotation and offset for all axis: