Program: 40098
Project: 40098
Buggy source:
public void process(APDU apdu){
  if (secureChannel == null) {
    secureChannel=GPSystem.getSecureChannel();
  }
  byte[] buffer=apdu.getBuffer();
  short length=apdu.setIncomingAndReceive();
  if (!apdu.isISOInterindustryCLA() && buffer[ISO7816.OFFSET_INS] != INS_GP_INITIALIZE_UPDATE && buffer[ISO7816.OFFSET_INS] != INS_GP_EXTERNAL_AUTHENTICATE) {
    ISOException.throwIt(ISO7816.SW_CLA_NOT_SUPPORTED);
  }
  final byte SC_MASK=SecureChannel.AUTHENTICATED | SecureChannel.C_DECRYPTION | SecureChannel.C_MAC;
  byte media=(byte)(APDU.getProtocol() & APDU.PROTOCOL_MEDIA_MASK);
  boolean contactless=(media == APDU.PROTOCOL_MEDIA_CONTACTLESS_TYPE_A || media == APDU.PROTOCOL_MEDIA_CONTACTLESS_TYPE_B);
  boolean isSecureChannel;
  if ((secureChannel.getSecurityLevel() & SC_MASK) == SC_MASK) {
    length=secureChannel.unwrap(buffer,(short)0,(short)(ISO7816.OFFSET_CDATA + length));
    isSecureChannel=true;
  }
 else {
    isSecureChannel=false;
  }
  piv.updateSecurityStatus(contactless,isSecureChannel);
  chainBuffer.processOutgoing(apdu);
  chainBuffer.processIncomingObject(buffer,apdu.getOffsetCdata(),length);
switch (buffer[ISO7816.OFFSET_INS]) {
case INS_GP_INITIALIZE_UPDATE:
    if (Config.FEATURE_RESTRICT_SCP_TO_CONTACT && contactless) {
      ISOException.throwIt(ISO7816.SW_SECURITY_STATUS_NOT_SATISFIED);
    }
  secureChannel.resetSecurity();
processGP_SECURECHANNEL(apdu);
break;
case INS_GP_EXTERNAL_AUTHENTICATE:
if (Config.FEATURE_RESTRICT_SCP_TO_CONTACT && contactless) {
ISOException.throwIt(ISO7816.SW_SECURITY_STATUS_NOT_SATISFIED);
}
processGP_SECURECHANNEL(apdu);
break;
case INS_PIV_SELECT:
processPIV_SELECT(apdu);
break;
case INS_PIV_GET_DATA:
processPIV_GET_DATA(apdu);
break;
case INS_PIV_VERIFY:
processPIV_VERIFY(apdu);
break;
case INS_PIV_CHANGE_REFERENCE_DATA:
processPIV_CHANGE_REFERENCE_DATA(apdu);
break;
case INS_PIV_RESET_RETRY_COUNTER:
processPIV_RESET_RETRY_COUNTER(apdu);
break;
case INS_PIV_GENERAL_AUTHENTICATE:
processPIV_GENERAL_AUTHENTICATE(apdu);
break;
case INS_PIV_PUT_DATA:
processPIV_PUT_DATA(apdu);
break;
case INS_PIV_GENERATE_ASSYMETRIC_KEYPAIR:
processPIV_GENERATE_ASSYMETRIC_KEYPAIR(apdu);
break;
default :
ISOException.throwIt(ISO7816.SW_INS_NOT_SUPPORTED);
}
}

Fixed version (ground truth):
public void process(APDU apdu){
  if (secureChannel == null) {
    secureChannel=GPSystem.getSecureChannel();
  }
  byte[] buffer=apdu.getBuffer();
  short length=apdu.setIncomingAndReceive();
  if (!apdu.isISOInterindustryCLA() && buffer[ISO7816.OFFSET_INS] != INS_GP_INITIALIZE_UPDATE && buffer[ISO7816.OFFSET_INS] != INS_GP_EXTERNAL_AUTHENTICATE) {
    ISOException.throwIt(ISO7816.SW_CLA_NOT_SUPPORTED);
  }
  final byte SC_MASK=SecureChannel.AUTHENTICATED | SecureChannel.C_DECRYPTION | SecureChannel.C_MAC;
  byte media=(byte)(APDU.getProtocol() & APDU.PROTOCOL_MEDIA_MASK);
  boolean contactless=(media == APDU.PROTOCOL_MEDIA_CONTACTLESS_TYPE_A || media == APDU.PROTOCOL_MEDIA_CONTACTLESS_TYPE_B);
  boolean isSecureChannel;
  if ((secureChannel.getSecurityLevel() & SC_MASK) == SC_MASK) {
    length=secureChannel.unwrap(buffer,(short)0,(short)(ISO7816.OFFSET_CDATA + length));
    length-=ISO7816.OFFSET_CDATA;
    isSecureChannel=true;
  }
 else {
    isSecureChannel=false;
  }
  piv.updateSecurityStatus(contactless,isSecureChannel);
  chainBuffer.processOutgoing(apdu);
  chainBuffer.processIncomingObject(buffer,apdu.getOffsetCdata(),length);
switch (buffer[ISO7816.OFFSET_INS]) {
case INS_GP_INITIALIZE_UPDATE:
    if (Config.FEATURE_RESTRICT_SCP_TO_CONTACT && contactless) {
      ISOException.throwIt(ISO7816.SW_SECURITY_STATUS_NOT_SATISFIED);
    }
  secureChannel.resetSecurity();
processGP_SECURECHANNEL(apdu);
break;
case INS_GP_EXTERNAL_AUTHENTICATE:
if (Config.FEATURE_RESTRICT_SCP_TO_CONTACT && contactless) {
ISOException.throwIt(ISO7816.SW_SECURITY_STATUS_NOT_SATISFIED);
}
processGP_SECURECHANNEL(apdu);
break;
case INS_PIV_SELECT:
processPIV_SELECT(apdu);
break;
case INS_PIV_GET_DATA:
processPIV_GET_DATA(apdu);
break;
case INS_PIV_VERIFY:
processPIV_VERIFY(apdu);
break;
case INS_PIV_CHANGE_REFERENCE_DATA:
processPIV_CHANGE_REFERENCE_DATA(apdu);
break;
case INS_PIV_RESET_RETRY_COUNTER:
processPIV_RESET_RETRY_COUNTER(apdu);
break;
case INS_PIV_GENERAL_AUTHENTICATE:
processPIV_GENERAL_AUTHENTICATE(apdu);
break;
case INS_PIV_PUT_DATA:
processPIV_PUT_DATA(apdu);
break;
case INS_PIV_GENERATE_ASSYMETRIC_KEYPAIR:
processPIV_GENERATE_ASSYMETRIC_KEYPAIR(apdu);
break;
default :
ISOException.throwIt(ISO7816.SW_INS_NOT_SUPPORTED);
}
}