For all intents and purposes, Warren Buffett, the CEO of Berkshire Hathaway (NYSE:BRK.A)(NYSE:BRK.B) is the greatest value investor alive. He may not be the richest man on the planet -- that's title currently belongs to Microsoft's Bill Gates -- but Buffett is by far the most adept investor of all time, given that, starting with less than $10,000, he was able to use his market smarts over six decades to turn that into what amounts to a nearly $61 billion net worth according to Forbes as of Feb. 15, 2016.

Buffett's secret recipe for success
What makes Buffett such a special investor? As discussed last year, some of Buffett's greatest attributes tend to fly under the radar. First, Buffett tends to focus on income generation and reinvestment. He likes companies that are perceived to be boring, where the products practically sell themselves. Boring companies can produce profits in any economic environment, which means dividends are paid to shareholders, and those shareholders can then reinvest back into more company stock. This compounding effect can lead to substantial wealth creation over time.

Secondly, Buffett has a knack for using dollar-cost averaging to his advantage. Buffett loves when his investments languish for years after a purchase because it gives him an opportunity to accumulate even more shares. He understands that investing isn't a sprint so much as a marathon, and he's prepared to nibble on businesses he likes on a regular basis.

Lastly, Buffett is an innovator rather than a follower. Following the beat of his own drum has allowed Buffett to capitalize in a big way. For instance, while many investors have chased the next big growth trend, Buffett has been busy adding consumer staples to his portfolio. Prior acquisitions by Berkshire Hathaway of Kraft Foods, Heinz, and BNSF demonstrate a focus on slower growth but steady demand products and services with strong brand power.

Image source: Flickr user Fortune Live Media.

Three stocks Buffett looks foolish for selling
Of course, not everything has gone Buffett's way. Despite being a wildly celebrated investor, Buffett has been wrong plenty of times as well. His most recent stinging loss came from U.K.-based grocer Tesco, which was never able to turn its business around, and Buffett's slowness to sell Berkshire Hathaway's stake caused it to take a hefty loss in the investment.

But it's not the actual losses that really sting Buffett. I'd be willing to bet it's the gains that he let get away that hurt him far more. There are three stocks Buffett has sold over the years that would have resulted in substantial gains had he continued to hold them. Instead, Buffett and his Berkshire management team took relatively quick gains, and paid quite the price in long-term opportunity costs.

Here are three stocks Buffett probably regrets selling in hindsight.

1. Home Depot (NYSE:HD)
One position the Oracle of Omaha probably wishes he could have back right now is do-it-yourself retailer Home Depot. Shortly after the end of the financial crisis in mid-2009, Berkshire Hathaway's quarterly filing's showed that the company's stake in Home Depot was cut by 25% from 3.7 million shares to 2,757,898 shares. Then, in the third quarter of 2010, Buffett's company completely sold out of Home Depot.  

Image source: Home Depot.

However, with hindsight being 20/20, we can see this was a poor move. Although information about the exact price Buffett received for he sold that Home Depot stock is unavailable, shares of the company traded for about $25 in mid-2009, and around $31 in Q3 2010. Shares of Home Depot closed this past week at $116.32 -- and that's not including the cumulative $8 per share in dividend payments shareholders would have collected between 2011 and 2015. All told, Buffett's roughly $93 million investment in the summer of 2009 would be worth more than $450 million today had he held on (a number that would be even higher after factoring in dividend reinvestment).

2. Lowe's (NYSE:LOW)
Buffett's exodus from do-it-yourself retailers extended into Lowe's as well, which was actually a bigger position for Berkshire Hathaway. During the fourth quarter of 2010, just one quarter after Berkshire disposed of its remaining stake in Home Depot, Buffett and his team sold all 6.5 million shares of its main rival, Lowe's. Based on the fact that he ditched both companies in such close proximity, Buffett and his team of advisors likely believed the housing rebound would be short-lived. That theory was proven wrong in a big way. 

Image source: Lowe's.

When Berkshire parted ways with his Lowe's stock, it was valued in the $22 to $25 a share range. The roughly 6.5 million shares owned by Berkshire were worth, at the high end, around $163 million. Unfortunately for Buffett and his advisors, Lowe's closed this past weekend just below $65. Furthermore, Lowe's is working on a 53-year streak of raising its dividend annually. Berkshire not only missed out on Lowe's stock more than doubling since Q4 2010, but $3.62 per share in cumulative dividends between 2011 and 2015. Had the company held on, its position would today likely be worth around $445 million, including dividends.

3. Disney (NYSE:DIS)
But, if you want to look at the pinnacle of the regrets in Buffett's storied investment history, look no further than his investment in Walt Disney in 1966. At the time, Disney had a theme park in Southern California and animated movies in its back pocket. The company was valued at roughly $80 million, and Buffett, liking what he saw, invested $4 million for a 5% ownership stake. Buffett wound up selling that stake a year later for a tidy 50% profit. 

Buffett's biggest "goof" of all. Image source: Disneyland.

However, if Buffett had held onto his original 5% stake, his position would be worth an insanely higher amount today. Based solely on where Walt Disney closed this past Friday, Buffett's shares would be worth more than $7.4 billion on a static basis. If we include dividends, Buffett would have also earned more than $9 per share on a spit-adjusted basis, or more than $700 million in extra income. In other words, we're up to an $8.1 billion mistake.

And yet it gets worse...

Thanks to the 1996 deal in which Disney bought Capital Cities/ABC, Berkshire "inherited" 21 million shares of Walt Disney stock. Once again, Berkshire and Buffett methodically disposed of its shares of Disney over time. On the day the deal was announced in 1995 (it didn't close until 1996), Disney was worth $16.05 per share on a split- and dividend-adjusted basis. Thus, the 21 million shares would have been worth about $337 million. Today's value for those shares would be $1.91 billion. Again, we don't know the specifics of how much Buffett received from the sale of these inherited shares, but I'd surmise Buffett and Berkshire wound up forgoing between $1.3 billion and $1.5 billion in extra profits based on Friday's closing price.

In total, Buffett's short-term thinking on Disney has cost his company well over $9 billion.

The most important lesson
Sometimes even the perceived-to-be-best investor in the world needs a reminder that trying to time the market just isn't a good move over the long term. In all fairness, Buffett has made far more right moves than wrong moves over his lifetime, and no one is perfect, so his mistakes are certainly forgivable. However, his biggest mistakes also serve as a reminder that having a big stock gain in the books isn't reason enough to cash in your chips if the investment thesis in a company still holds water.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.