Is it a common problem for a refinance appraisal to come in low because there aren't enough comparable homes available?

It depends heavily on location; comp scarcity is a real problem in some areas and a non-issue in others. In a densely built tract neighborhood, there are usually plenty of comparable sales even when overall volume is low, so the appraiser has good data to work with. In a rural area with one house per mile and every property different, finding genuinely comparable sales can be legitimately hard, and that is where low or difficult appraisals show up. Unique properties hit the same wall. We recently worked on a home with an ADU that worried us for exactly this reason, because there was little to compare it to, though we got fortunate and found a couple of solid recent sales. The way to get ahead of it: pull an automated valuation model before ordering the appraisal, so you can see everything that has sold nearby and tighten the comparison by square footage, distance, and time. That tells you whether the comps exist to support the value you are expecting. One honest caveat. Nearly every homeowner believes their home is the nicest within miles, and that is rarely true, so comps almost always need adjustment for quality, size, lot, and amenities. A realistic read on where your home actually sits keeps a low appraisal from catching you by surprise.