Table was not found and Invalid Topology using Geoprocessing Clip

[MaureenDeJesus]

I have a shapefile and a land cover map. The shapefile is WGS 1984 while the Land Cover is in Web Mercator, but they align with each other in the viewer. I am trying to clip the Land cover to the same as the shapefile. But every time I tried, the error table was not found or an invalid topology arose. I tried clipping with the same projection but there is still an error in the extent. 

[Lee_Butler]

Have you tried running the repair geometry tool on the shapefile before running the clip to make sure there are no geometry errors in the data?

[MaureenDeJesus]

I did but there is still an error 000117, the output empty generated