According to the WhatsApp encryption overview as published on: https://www.whatsapp.com/security/WhatsApp-Security-Whitepaper.pdf - WhatsApp is using the GPL version 3 licensed software (https://github.com/signalapp/libsignal-protocol-java) in their application which is proprietary.
It seem to be a violation of GPL 3 license.
The Open Whisper Systems who is author of that software seem to be fine that Facebook's WhatsApp may use in their proprietary software, yet it is contradiction to what free software shall be and how it shall be used.
It is a new opportunity to make the WhatsApp software truly free, at least all those versions which used the GPL 3 licensed software in past.