I've never heard of rust being a problem in Monkey Puzzle trees. Could you give a more detailed description of the problem, or, better yet, post pictures?

Am with Tugbrethil, never heard of rust on Monkey Puzzle, so a pic would help. The bottom branches go brown with age and then fall off (if not sawn off) - so I wonder if it might just look like rust or mould as it is dead and needs taken off, am thinking out loud really.

Drought (or frost!) damage can turn the leaves rusty brown, too.

its very common for monkey puzzles to have brown parts like the stem or lower branches . i have 2 and they both have brow parts but there fine and growing well . monkey puzzles are one of the oldest living things on the planet in the form there in now basicly . they were just assumed to stop monkies climbing them as they dont ever mi in the wild and th tree has been around much much longer than any dinosaur let aone monkey . if your tree seams healthy it probably is .