Consider the following test files:
-----IncorrectWarning.java:
public class IncorrectWarning {
    private Aux a;
}
-----
-----Aux.java:
import java.io.StringBufferInputStream;

public class Aux {
}
-----

When the deprecation warnings are enabled, there should be a warning produced for the import in the Aux class, like this:
-----
$ javac -sourcepath . -Xlint:deprecation Aux.java IncorrectWarning.java
Aux.java:1: warning: [deprecation] StringBufferInputStream in java.io has been deprecated
import java.io.StringBufferInputStream;
              ^
1 warning
-----

But when compiling the IncorrectWarning.java first, the warning is incorrectly put into the IncorrectWarning.java file:
-----
$ javac -sourcepath . -Xlint:deprecation IncorrectWarning.java Aux.java
IncorrectWarning.java:1: warning: [deprecation] StringBufferInputStream in java.io has been deprecated
public class IncorrectWarning {
              ^
1 warning
-----

This is reproducible with jdk8/tl/langtools tip:
$ hg tip
changeset: 1890:37031963493e
tag: tip
user: jjg
date: Fri Jul 12 13:11:12 2013 -0700
summary: 8020278: NPE in javadoc

Also reproducible with:
$ javac -version
javac 1.7.0_11