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Hey bonsai buds. Hoping you all might help me id what is going on my leaves! See pictures below.

My Fukien Tea Tree is doing relatively well. It has acclimated to its new home and light, Ive had a couple leaf turn overs but there is new growth and blossoms, so it seems ok. But there are these orange-ish spots on many of the leaves which slowly turn brown over time, meanwhile the unaffected parts seem fine. The lesions seem slightly raised. I treat with Neem oil the prevent mold, but that hasn’t prevented or even slowed down development on previously pristine leaves.

Some kind of fungi?
Black Spots are usually the easiest to occur in Carmonas, but I couldn't find a match for exactly the same spots your tree is showing.
Try a fungicide and keep it out of direct sun for a some days, see if it helps.