What probably happened
The skin wasn't dry enough before roasting, the oven wasn't hot enough at the end, or you covered the pork the whole time.
Why it happened
Pernil is a slow-roasted pork shoulder with the skin on. The skin's job during roasting is to convert from rubbery collagen into glassy, crisp crackling. That conversion requires three things: dryness, salt, and high heat at the end. Skin is mostly water, collagen, and a small amount of fat. To crisp, the water must evaporate completely — but if the skin is wet when it goes in the oven, that moisture turns to steam and steams the skin instead of crisping it. Salt on the skin draws out surface moisture through osmosis, creating a dry surface. And the final blast of high heat (425°F–450°F) is what puffs and crisps the dehydrated collagen. If you roast covered the whole time at 325°F, the trapped steam keeps the skin rubbery.
How to save it now
If the pernil is already cooked with soft skin, remove the skin in one piece, score it, and lay it flat on a baking sheet. Broil on high for 3–5 minutes, watching constantly. It'll puff and crisp into chicharrón-like crackling. Chop and serve on top of the sliced meat.
How to prevent it next time
The night before: score the skin in a crosshatch pattern, cutting through the skin but not into the meat. Pat the skin completely dry. Rub it generously with salt — the salt should sit visibly on the surface. Leave the pork uncovered in the fridge overnight. The dry fridge air plus the salt will dehydrate the skin. Roast at 325°F, uncovered, until the meat is tender. Then crank the oven to 450°F for the final 15–20 minutes with the pork positioned near the top of the oven. The skin will blister and crisp.
Tiny kitchen test
Buy a pork shoulder with skin on. Salt one half of the skin and leave it uncovered in the fridge overnight. Leave the other half unsalted and covered in plastic. Roast both together. The salted-dried half will puff into glassy crackling. The covered-unsalted half will stay soft and rubbery.
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