I am familiar with and have used GEDMatch occasionally since v1.03 was released nearly a decade ago. However, the software is designed to compare two GEDCOM files, not repair errors to a database structure.
When you wrote " it seems to me that if you have two or three different individuals in your file who are really the same person then your file is in error' you were writing about data entry errors. A data entry error is when the user types '1980' instead of '1880', types the wrong spelling of a name, or enters the same person twice. FTM has a report that can be run where the user can select which data entry errors should be checked for and identified.
On the other hand, an error to the database structure is not user error. For example, after compress failed I discovered a person born in the 1800s was connected as a child to a person born in the 1960s. Checking the original file from which the data had been transferred to FTM I found that link did not exist. I also checked the original GEDCOM used for that transfer (use GENViewer for that) and found the linkage was not in the GEDCOM. I also found other database linkage errors created by FTM when compress failed. Unfortunately, there is no was in FTM to check for errors in the database structure and correct those errors.
Typically database software has options within the software to check for database structure errors, typically with those errors being fixed. Looking at another software on this computer, it has Refresh Data (checks and updates date ranges), Check Field Codes, Check Links, Repair Database Structure, and Compact Database. Those options were designed to check for problems with the database structure and fix problems found. The software contains a separate report that checks for user data entry errors similar to the report found in FTM.