Indeed the description of your problem is vague...
However, a common problem with dynamic VIs in executables is that their front panels are not saved by default by the application builder, generating run-time errors when attempting to open panels. Go in the VIs settings and check for saving FP of each VI that you open dynamically.
If you want that your application open VIs on double-clicks in the Explorer, add the line
RegisterExtensions = True
in the application INI file.