One disadvantage of organic food is that it can be difficult to find. Your area may not have a farmer's market and your local stores may only carry a limited selection. Thankfully, these things are expanding drastically in recent years, but we still have a ways to go and this means a little extra work on your part, either finding good sources, ordering in bulk or growing and/or raising our own.
Another hindrance to the advantages of organic food I think I hear often is that the selection is just naturally limited, not just because stores don't stock it, but because the organic counterpart to a conventional food just isn't made. And this is true for multiple reasons. First, some foods are just plain crap and can't be made healthy or organic without a bonafide miracle. The second is that organic foods tend to be seasonal, since they aren't genetically modified to withstand cold and aren't usually grown unnaturally (such as in hothouses). This means it's going to be hard to get something like fresh tomatoes in January, or asparagus in the heat of summer.
The most common complaint though is that organic food is too expensive. And this seems accurate when you're comparing it in your grocery store to conventional food.
But it's important to understand that what IS organic isn't actually more expensive; non-organic food has just been made artifically cheap by government farm subsidies.