I am attaching a Java file to reproduce the problem.
Follow these steps to reproduce the problem.

1) javac -g -d classes pkg/Bar.java
2) cd classes
3) $JAVA_HOME/bin schemagen pkg.Bar

You will get something like this
D:\fresh\classes>%JAVA_HOME%\bin\schemagen pkg.Bar
error: The type of the getter is java.util.List<java.lang.Integer> but that of t
he setter is java.util.List. They have to be the same.
        this problem is related to the following location:
                at pkg.Bar.getNumbers (Unknown Source)
                at pkg.Bar (Unknown Source)
        this problem is related to the following location:
                at pkg.Bar.setNumbers (Unknown Source)
                at pkg.Bar (Unknown Source)
1 error

The same file when compiled without debug option works fine.
Seems Schemagen is getting different information from the class file when compiled with debug option.