Answer: Yellow spots may indicate fungal diseases, but there are many possibilities and based on your description I can't be sure exactly what's causing them. Cedar-apple rust begins as yellow spots with a dark center. The spots eventually turn orange. If this is what's happening, you'll want to put your tree on a preventative spray schedule, using a fungicide every 7-14 days. Begin spraying when the flower buds turn pink (but before they open). You'll find more detailed instructions on the fungicide label. Best wishes with your tree.
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