DIAGNOSIS Those are likely just spots where the natural aluminum oxide layer has been disturbed or where minor pitting has occurred from contact with acidic or salty foods. Pure aluminum is very reactive, and this is a common appearance after use.
FIX It's probably still safe functionally. Clean it well with hot, soapy water and a non-abrasive sponge. To help protect it, you can "season" the interior: after cleaning, dry it thoroughly, then heat it on the stove with a couple tablespoons of cooking oil inside, swishing it around until it smokes lightly. Let it cool, then wipe out excess oil. This creates a thin, polymerized layer that can reduce further direct contact.
IF THAT DIDN'T WORK If the pitting is deep, numerous, or you can actually feel holes, the structural integrity might be compromised. Aluminum can corrode through if exposed to strong chlorides (like canning salt without a protective liner of water) or stored damp. If you're in doubt, retire it.
HEADS UP Always use the recommended amount of water in the bottom to create a buffer between the jars and the metal. Never store food directly in the canner, and always dry it completely after washing. Avoid using harsh alkaline cleaners (like some dishwasher detergents) or leaving acidic residues (tomato sauce, vinegar) sitting in it for long periods.