Do you have a battle video? :)
Based on your narration, this is what seems to have happened.
1. Unnamed Pokemon was fainted by your Crawdaunt and Lickilicky.
2. Crawdaunt and Lickilicky took Sandstorm hits.
3. Opponent's Lickilicky came in and Cloud Nine activated, canceling Sandstorm.
Sandstorm deals damage at the end of a turn and before new Pokemon come in.