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we may never know, only guess, gwaine did wish him luck in finding what he was looking for, but i dont think he realised it was the crystal cave and magic, and when gaius returned and said to gwen not to send the knights because morgana's army were everywhere, not because merlin was magic, and by the time gaius cryptically told gwen, gwaine and percival were off to find morgana, so no, i think he may have been suspicious that merlin was not actually collecting herbs, but no one's really sure if he knew or not.