These are some iffy ones:
Brass instruments, brass section, or is that too broad? There must be others with “brass.”
Mints, at least the natural/original ones were made from mint.
Diamonds are called rocks, slangily.
Furs (like a mink coat) are made of animal hides.
Opium is a close one. It is made from the opium poppy, but we don’t call the drug “poppy.”
Crystal, as in a fine crystal vase. I think that’s a good one.
I was going to say that glass can refer to cubic zirconium, but that’s made of aluminum silicates, not glass.
Forgive me if I’m wrong, but I thought that pencil lead was never actually made out of lead (Pb)? They were instead made out of graphite, which is carbon. I think you’d be hardpressed to write something with Pb, especially considering how valuable it’s been for most of history.
How about sponges or loofahs? Catgut? Kentucky Fried Chicken?
gotpasswords, as far as I know, my reeds are still made out of, um, reed. There are plastic reeds, yes, but they are far less common than ones made out of reed.
Brass: As slang for military officers, it’s metonymy for their brass insignia of rank. But even closer is the fact that the brass plaques showing coats of arms, bas relief faces, etc., that are posted above the burial sites of people interred within churches, are called “brasses.”
Lead, as in pencils: Owing to visual and tactile similarities, lead may mean graphite as well as element 82.
Canadian nickels used to be 100% nickel. Now they are an alloy, I think the same one as US nickels, but I’m not sure.
Another one for iron: tire irons.
Someone suggested ‘pigskin’ for a football, but footballs were never made of that. They originally were made of a pig bladder, but for some reason no one calls them a pig bladder…
It’s a little-known fact that the Great Wall of China is actually constructed out of fine porcelain. It’s also the only man-made object referred to by the material it is made from that is visible from outer space.
Paintings are often called “oils” or “acrylics,” depending on the type of paint that was used. The paints themselves are also called “oils” or “acrylics,” based on their ingredients.
And a drawing can be a “pastel” or a “pen and ink,” etc.
Violin (and other) strings are often called “catguts,” though I hope none of them still contain any actual gut of cats.
Dentures are sometimes referred to as “ivories.”
“Neon” lights may or may not contain actual neon.
Some pickles are “dills” (or “kosher dills”), because that’s one of the herbs/spices used in their production.
Is the “chrome” on a car still made of chromium?
Bread can be known by the type of grain in contains, e.g. “ham and swiss on rye.”
Audio cassettes (and sometimes even digital media) are called “tapes.”
It’s a less known fact that millions of apples were consumed during the construction of New York, hence its name “the Big Apple”. This is the only man-made fruit that is visible from outer space.
Actually most fish sticks are made with pollock, an actual fish. It’s an interesting phenomenon that the most widely consumed fish is one that most people couldn’t name.
Which reminds me that violinists often refer to the non-wooden part of the bow as the “horsehair,” even if it’s made from a synthetic substance.
And the strings are often referred to as “catgut,” when, so far as I know, there is never any cat involved – it’s either made from sheep’s intestines or some synthetic material.
As has been noted in a recent thread about saxophones, “woodwinds” are often made from metal or plastic, particularly saxophones, flutes, and clarinets.
Miniatures used for table-top wargaming or role-playing games are “leads,” even if they’re made from something other than lead.