According to the article, it’s not the completed tunnels, but rather, the dig sites. It’s mostly normal digging byproduducts (silt, rock dust, sand, water), but also chemicals for making/setting grout. All of that stuff is “normal”, but the outrageously lax safety standards have let it build up rather than be dealt with.

“Elon Musk Tunnels Oozing with Skin-Burning Chemical Sludge” is a sensationalist clickbait take. “Elon Musk’s Tunnels-In-Progress Full of Improperly Stored/Disposed-Of Dangerous Chemical Waste” wouldn’t spark the imagination so hard.