dex2jar error: handleHotSwapPatch + FragmentManagerImpl

Question

I tried to access codes of my deleted app by apk got from emulator. I accessed classes.dex but there is a problem making it jar by dex2jar. This is really important for me, how to fix that? The error file below:

Summary

version: reader-1.15, translator-0.0.9.15, ir-1.12
there are 2 error methods
options:  -d

t0.txt

  java.lang.NullPointerException
        at com.googlecode.dex2jar.ir.ts.LocalSplit.transform(LocalSplit.java:255)
        at com.googlecode.dex2jar.v3.V3MethodAdapter.visitEnd(V3MethodAdapter.java:215)
        at com.googlecode.dex2jar.v3.V3ClassAdapter$2.visitEnd(V3ClassAdapter.java:320)
        at com.googlecode.dex2jar.reader.DexFileReader.acceptMethod(DexFileReader.java:691)
        at com.googlecode.dex2jar.reader.DexFileReader.acceptClass(DexFileReader.java:436)
        at com.googlecode.dex2jar.reader.DexFileReader.accept(DexFileReader.java:323)
        at com.googlecode.dex2jar.v3.Dex2jar.doTranslate(Dex2jar.java:85)
        at com.googlecode.dex2jar.v3.Dex2jar.to(Dex2jar.java:261)
        at com.googlecode.dex2jar.v3.Dex2jar.to(Dex2jar.java:252)
        at com.googlecode.dex2jar.tools.Dex2jarCmd.doCommandLine(Dex2jarCmd.java:110)
        at com.googlecode.dex2jar.tools.BaseCmd.doMain(BaseCmd.java:174)
        at com.googlecode.dex2jar.tools.Dex2jarCmd.main(Dex2jarCmd.java:34)
DexMethodVisitor mv=cv.visitMethod(ACC_PRIVATE, new Method("Lcom/android/tools/fd/runtime/Server;","handleHotSwapPatch",new String[]{ "I","Lcom/android/tools/fd/runtime/ApplicationPatch;"},"I"));

t1.txt

  java.lang.NullPointerException
        at com.googlecode.dex2jar.ir.ts.LocalSplit.transform(LocalSplit.java:255)
        at com.googlecode.dex2jar.v3.V3MethodAdapter.visitEnd(V3MethodAdapter.java:215)
        at com.googlecode.dex2jar.v3.V3ClassAdapter$2.visitEnd(V3ClassAdapter.java:320)
        at com.googlecode.dex2jar.reader.DexFileReader.acceptMethod(DexFileReader.java:691)
        at com.googlecode.dex2jar.reader.DexFileReader.acceptClass(DexFileReader.java:441)
        at com.googlecode.dex2jar.reader.DexFileReader.accept(DexFileReader.java:323)
        at com.googlecode.dex2jar.v3.Dex2jar.doTranslate(Dex2jar.java:85)
        at com.googlecode.dex2jar.v3.Dex2jar.to(Dex2jar.java:261)
        at com.googlecode.dex2jar.v3.Dex2jar.to(Dex2jar.java:252)
        at com.googlecode.dex2jar.tools.Dex2jarCmd.doCommandLine(Dex2jarCmd.java:110)
        at com.googlecode.dex2jar.tools.BaseCmd.doMain(BaseCmd.java:174)
        at com.googlecode.dex2jar.tools.Dex2jarCmd.main(Dex2jarCmd.java:34)
    DexMethodVisitor mv=cv.visitMethod(ACC_PUBLIC, new Method("Landroid/support/v4/app/FragmentManagerImpl;","allocBackStackIndex",new String[]{ "Landroid/support/v4/app/BackStackRecord;"},"I"));

addition: I got the apk from installed project by pull command and it doesnt signed. Normally, I have not even seen this error with signed apks.