The lines which instantly come to mind are
Here comes a candle to light you to bed
Here comes a chopper to chop off your head
I know that "Ring around the Rosy" was written about the plague...back in high school, in an EngLit class, we had a few classes about children's lit through the years. It's always been on the bloody side, that's not a recent phenomenon.
In the original Cinderella, one step-sister cut off her toe to fit her foot in the slipper, the other cut off her heel.
Oh, Mother Goose is way scary. I wasn’t arguing with you.
All those older things have been cleaned up for current readers.
Rock a bye Baby ain’t exactly a happy lullaby either.