I recently downloaded the entirety of the SGMC dataset from the USGS site. The website for this data is at https://www.sciencebase.gov/catalog/item/5888bf4fe4b05ccb964bab9d. I selected the shapefile zip file version of the data. Within that zip file is a file entitled "SGMC_Geology.shp". So far so good. When I displayed that in the map view everything displays correctly. This is where the good news ends.
I tried to clip this file to some state boundary data I had previously downloaded from the state of South Dakota. The clipping happened very fast and I discovered that the resulting shape file output was entirely empty. No data and no tables. I noticed a message that indicated the geometry in the source file was not correct. So I ran the QGIS fix tool(using the structure option), redisplayed the data and was rewarded with a proper display. When I again clipped to the South Dakota border shapefile I again obtained an empty result.
I then selected all of the South Dakota entries in the original fixed SGMC shapefile, exported them using the 'export selected' option on the layer and was rewarded with a complete file. But, the exporting option resulted in file with 'invalid projection' when it should have contained the original 102039 Albers projection. This was very frustrating.
I ran the assign projection tool and it failed and left the layer with an invalid projection. So I removed the layer and reselected the clipped SGMC file and the layer yielded a "?" to the right of the layer name. I clicked on this and assigned "102039" as the projection and "magically" it projected onto the state boundary shape in my project(which was using a 32614 projection. And by the way this answering session for the "?" asked me to select the projection method from one to the other. I selected the top option and it worked.
So, is QGIS flakey, or is the SGMC shapefile flakey, or is the reprojection tool not working properly or is the fix tool not working properly or is the export selected features not working properly.