The Inno Setup does not modify the installed EXE files in any way.
If the application is failing when installed, it's not Inno Setup's fault per se, it's rather fault in the deployment process.
Possible reasons why the installed application is failing are numerous, including, but not limited to:
- You omitted some dependency
- DLL library
- .NET Framework
- Java Runtime Environment
- other runtime
- COM/ActiveX object, etc.
- The application requires some configuration
- a file
- a registry key [including COM/ActiveX object registration]
- an environment variable, etc.
- Some applications require a write access to their folder. As Inno Setup installs the application to "Program Files" folder by default, where write access is restricted, such applications fail.