Going off what I heard from a podcast guest I trust, rust spots like that when using LEDs are possibly due to lack of calcium, as LEDs can make your plant require extra calcium. I'll see if I can link the episode, it's a fantastic one I have listened to it 3 or 4 times already.
Episode 21: Seedlings, Soil & Synthetics w/ Dan (Full Duplex) – Autoflower Podcast
autoflowerpodcast.com
Podcast episode I referenced, great episode and great podcast in general.