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I'm trying to do a union between two Polygon Shapefiles, but when I do Vector > Geoprocessing Tools > Union I have the odd issue where most of it works fine, but some areas are returned in the union dataset as being a gap, but there is data there in both input files.

Here are some pictures to show you what I mean.

Input 1: enter image description here

Input 2: enter image description here

Union Output: enter image description here

Union Output overlaid on the input layers: enter image description here

To help identify the issue, they're both in the same CRS and are both Polygon format Shapefiles, and the geometry of the polygons in the input data where a gap is being created look fine under inspection.

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It looks like one polygon on the red layer is being eliminated from the output. My guess is that the output of that area is a self-intersecting polygon.

Here are a few things you can try:

  1. Look for places where the problem polygon intersects vertices of the green layer. Adjust the geometry of the problem polygon so it won't create a self-intersecting polygon.
  2. Select that polygon on the red layer, and run the union using only selected features for the red layer. If this works, use Select by location to select features in the new union layer that intersect the problem polygon, and paste the selection into the original union layer.
  3. Select the problem polygon, and use it to clip the green layer. Run the union tool on the clipped layer, and paste the output into the original union layer.
  4. Use the Intersection and Symmetrical Difference tools instead of the union tool. Combine the outputs into one layer.

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