qgis - Can't clip point shapefile with missing attribute data

I am having trouble clipping a point shapefile to with a polygon shapefile in QGIS 2.18.2. I was able to clip a point shapefile from a different source successfully (using the same polygon) so I think the point shapefile is the issue. I also tried the intersect tool but both provided the same message in the log:

"Algorithm clip starting...

1004 See log for details"

The presumably problematic data was downloaded as a KML file from:

http://ucjeps.berkeley.edu/cgi-bin/get_consort.pl?county=&source=&taxon_name=camissonia%20campestris&collector=&aid=&year=&month=&day=&loc=&coll_num=&max_rec=2000&make_tax_list=&before_after=&last_comments=&VV=&non_native=0&geo_only=&geo_no=&CNPS_listed=0&weed=0&sugg_loc=&tns=&lo_e=&hi_e=&YF=0&VTM=0&baja=0&georef_only=1

One difference that is apparent between the two shapefiles is that the one that works has a normal, complete attribute table, while the problem shapefile has an attribute table that looks like this:

I converted the file to shapefile in QGIS but both the KML and shapefile attribute tables look the same.

If this is the reason I can't clip this shapefile, is there is a way to get the KML file to show the attribute data properly?

If this issue can't be resolved for this file, the data can also be provided as a tab separated list, however, I am having issues getting this into a usable form (or I wouldn't be asking this question), so I will post a separate question to resolve that problem if necessary.