Patrick Foote of Name Explain compiled an amusing list of common words used in the English language with unknown origins. Foote used examples from a wide range of subjects including gender (boy, girl), animals (dog, rabbit toad), food (mushroom, cheese, jam), various sundries (spoon, cup, clock), and other (flag, gadget, chump). Foote also provides a wide caveat as to what he considers to have unknown etymology.
I also need to clarify that for many of these words we do kind of know where they come from, as then we know the older words they came from. Like we might know an English word comes from an old Latin word, which then turn came from an old Greek word. But we don’t know where that old Greek word came from.