When I first heard this saying several years ago, I didn't understand it either! Some sayings are just weird...
"Sometimes you have to just stop and smell the roses." The woman said to Castiel with a shrug and left. Wait, what? Castiel thought, confused. What does smelling flowers have to do with becoming a more relaxed person?
Dean had told Castiel one to many times that he was to serious and never relaxed, so they had tried teaching him humor, which had dismally failed when he couldn't even get angelic jokes. So they had given up, but Castiel had continued thinking about to it. So he'd just asked a random woman walking by what to do to become more relaxed. She had looked at him like he was insane, and that had been her reply before leaving.
Castiel really didn't understand. He decided, however, that Dean might like him better if he was more relaxed, and he really wanted Dean to like him and rely on him even more, so he thought he'd better try out the advice. He teleported away when no-one was looking at him and appeared in someone's garden. It was laden with rose bushes.
The angel went over to a red rose bush and, hesitantly, leaned down and inhaled. So what? It smelled like a flower and he felt no calmer. Confused he reached to pick it, and drew his hand back sharply. Did something just bite him?
He knelt and peered into the bushes, but made out nothing. When he looked back at the rose he realized what it had been. Big thorns stuck out of the rose's stem! Carefully, Castiel picked it, then as an afterthought he tore off the thorns.
He put it to his vessel's nose and smelled it again, but he STILL didn't feel any different. Thoroughly confused, he disappeared to talk to Dean.
When he appeared in their hotel room holding a rose, the brother's looked at him strangely. "That for me?" Dean asked sarcastically, looking back to his magazine.
Castiel looked down at it. Why had he brought the thing along? "I don't know." He said.
"Why do you have it?" Dean asked.
"Well…" Castiel wasn't entirely sure himself. "Sometimes you just have to stop and smell the roses."
Dean raised his eyebrows, but let the obviously misunderstood saying pass without comment.