This is strange. I pasted the relevant parts of the static initialization block of o.h.v.u.Version in a class with a main and added some poor man's logging traces:
public class VersionTest {
    public static void main(String[] args) {
        Class clazz = org.hibernate.validator.util.Version.class;
        String classFileName = clazz.getSimpleName() + ".class";
        System.out.println(String.format("%-16s: %s", "classFileName", classFileName));
        String classFilePath = clazz.getCanonicalName().replace('.', '/') + ".class";
        System.out.println(String.format("%-16s: %s", "classFilePath", classFilePath));
        String pathToThisClass = clazz.getResource(classFileName).toString();
        System.out.println(String.format("%-16s: %s", "pathToThisClass", pathToThisClass));
        // This is line 39 of `org.hibernate.validator.util.Version`
        String pathToManifest = pathToThisClass.substring(0, pathToThisClass.indexOf(classFilePath) - 1)
            + "/META-INF/MANIFEST.MF";
        System.out.println(String.format("%-16s: %s", "pathToManifest", pathToManifest));
    }
}
And here the output I get when running it:
classFileName   : Version.class
classFilePath   : org/hibernate/validator/util/Version.class
pathToThisClass : jar:file:/home/pascal/.m2/repository/org/hibernate/hibernate-validator/4.0.2.GA/hibernate-validator-4.0.2.GA.jar!/org/hibernate/validator/util/Version.class
pathToManifest  : jar:file:/home/pascal/.m2/repository/org/hibernate/hibernate-validator/4.0.2.GA/hibernate-validator-4.0.2.GA.jar!/META-INF/MANIFEST.MF
In your case, the StringIndexOutOfBoundsException: String index out of range: -2 suggests that: 
pathToThisClass.indexOf( classFilePath )
is returning -1, making the pathToThisClass.substring(0, -2) call indeed erroneous.
And this means that org/hibernate/validator/util/Version.class is somehow not part of the pathToThisClass that you get. I don't have a full explanation but this must be related to the fact that you're using One-Jar.
Could you run the above test class and update your question with the output?