I once quoted a line from a well-known commercial jingle in a story I published in Seventeen Magazine and Seventeen wouldn't publish it until I sought and gained permission for that use from the rights holder.
That was on me, not on my editor at Seventeen.
I was able to secure the right to use it -- but it wasn't easy. I had to send the department in charge of granting permission the entire story so they could evaluate whether they wanted to sign off on this use of their lyric.