I am using SAGA's Clip Raster with polygon tool in QGIS 2.18.4. It is missing an entire row of cells which are entirely contained within the clipping polygon (see image, original DEM in colours, clipping polygon in red outline, output in greys - just looking at the very top of the polygon).
I have checked my project and layer CRSs are all the same. I also considered using gdal's "Clip raster by mask layer" but found SAGA's easier for the batch processing as I'm running this for many different layers so would prefer to stick with SAGA if possible.
Does anyone know what's going on here?