Usually that's because of under-extraction. The acid in the coffee is always the first component to be extracted, and if the coffee is not brewed enough, the oil and fragrance would not be extracted completely, leaving you with an unbalanced ratio of acid in your coffee. 

The most common fix for this is to use a finer grind of coffee designed for pour-over, as finer grinds have larger surface area, making the coffee flavors easier to extract.
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