I'm posting this here so that anyone else experiencing this problem might stumble on this for a solution. I have a map containing (among other things) a vector layer opened from a .zip archive using the browser and a raster layer. When I try to clip the raster with the vector I get "The following layers were not correctly generated." I checked and I didn't have spaces in file names or any of the other common sources of problems. Then it dawned on me that qgis was just handing off the task to gdal, which doesn't know how to read inside a zip archive. I extracted the vector layer from the zip archive and my problems disappeared. So, if your clip is failing, this could be your problem.
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