I have a set of 1000 urban points that I'm trying to intersect with a classification result to find the accuracy but I keep getting an error "GEOS geoprocessing error: One or more input features have invalid geometry."
Double check your feature table to make sure that all of features have geometry/shape data associated with them.
If all features appear valid, have you tried resetting the CRS?
Reset the CRS. Go to Settings>Project Properties> CRS and Set a Reference system again. This should do the job. If not, export it as an ESRI shapefile.