Quality control checking in GIS falls under two main categories, geometric and tabular. Since GIS workflows are not standard your QA/QC process is unique to your case.
In general most proprietary and open source GIS applications have a set of tools that check for geometric errors (e.g. ArcGIS Checking and Repairing Geometries, QGIS Check Geometry Validity, or GRASS v.clean).
Imputing tabular data workflow should start with creating domain within your database. This will help prevent errors in attribution. For example in ArcGIS you can set up domains on geodatabase feature classes and tables (Attribute Domain), in QGIS you can setup attribute list.
In both categories creating scripts or tools that are unique to your situation may also help check for both geometric and tabular errors. I would recommend learning python which is utilized in both ArcGIS and QGIS.