Strange Hydro Contours

Hello

I am having trouble with the hydro contours ORD creates when using shapefiles of CSVs that were created in a different software such as QGIS. 
Some of the hydro contours contain 'loops' as shown in the screenshot below:

Does anyone know what causes this 'looping'? How can I prevent this?

Editing the terrain model is time consuming and does not always remove the loops.