I am using QGIS 2.12.3
I have two layers, one a complete grid of 1km squares, the other polygons representing urban land.
Whether I intersect clip or difference these two layers, some of the km squares are omitted from the new layer. It can't be a data issue as the missing squares are different depending on which operation I undertake, although they appear consistent for each operation.
Can anyone explain - I must admit I find the geoprocessing tools can often ignore a polygon on an layer with no obvious reason (yes I have tried validating the layers with no errors).
Note how the same polygon interacts properly with many other squares.
The polygon does fail validation but I have been around the periphery of failed squares and can see no faults.