There is a fungus issue and it will never go away if kept on the ground. There is too much of a microcosm at the ground from water run off from watering that always keeps the plant in a danger zone for multiplication of fungus spores. Get the plant elevated on some benches or a stand at least two feet off the ground 18" minimum and next year will be better. The leaves on the tree are tainted from fungus and will not get better and this time of year the trees are usually exhausted from the summer and will be pretty tattered looking, couple that with shitty leaves from fungus and they look like Hell. In my climate, (have no idea about yours) I can take off all the leaves right now, and I will get a second spring here in about two weeks. Start spraying fungicide alternating with copper and Bayer 3 in 1 once a week weekly till the leaves come out. Then monthly after that for the next few months and then every other month for the rest of it's life. Yes, I said the rest of it's life. Thought bonsai carried no maintenance didn't ya. It's all about maintenance and if you let up the tree will show you....and it usually ain't pretty!
good luck, your tree is fine, just needs some TLC