It's no secret that owning shares of Whole Foods (Nasdaq: WFM) stock has been a great long-term investment for many investors. But while the company has helped redefine what the grocery shopping experience can be, it has run into troubles as of late.

Before diving in, it's worth noting that I recently talked about three reasons I thought the company's stock could go up in the future here.

A Whole Foods Market in North Miami. Source: Ines Hegedus-Garcia, via Flickr

While I outlined reasons I thought the stock could rise in my previous piece, its important to note the bearish arguments against Whole Foods. With that in mind, here are three major concerns Whole Foods investors should be aware of moving forward.

Comps slowing
There is, perhaps, no metric more important for grocery chains than comparable-store sales, or comps. Because just about anyone could grow sales by simply adding more stores, looking at revenue growth doesn't always tell the whole story.

Comps, on the other hand, give a more detailed picture by comparing how the average store did this year, when compared to last year. New stores are not included in the equation. This metric lets investors know if a store's concept is catching on with consumers or not. It also signals when some stores have entered the phase where they have hit market saturation.

On the whole, any large grocer that is able to grow comps faster than inflation is considered a success. For years, Whole Foods was posting numbers far higher, and the stock responded with similar rises. Lately, however, those numbers have been coming in lower, causing Wall Street to worry about saturation, and the effects of competition.

Source: SEC filings. 2014 results are from the company's first three fiscal quarters. Years 2011 to 2013 are for full fiscal years.

Part of this is understandable: as a company's base of stores grows larger and more mature, comps eventually have to come down. But management has mentioned that growing competition has something to do with it, and it's that competition that has investors worried.

Speaking of competition
When Whole Foods began offering up natural and organic food in the late 1970s, there wasn't much competition. In fact, lots of people thought the idea of a grocery store with such a focus going public was ridiculous. Since then, however, the stock has returned 2,790%.

They say that imitation is the most sincere form of flattery. But you could forgive investors for not being too flattered at the spate of grocers following Whole Foods' blueprint into the natural/organic market. Sprouts Farmets Market (NASDAQ:SFM), Natural Grocers (NYSE:NGVC), and The Fresh Market (UNKNOWN:TFM.DL) have publicly stated that they can eventually have 1,200, 1,100, and 500 locations nationwide, respectively. Whole Foods currently has 389 stores, but believes it can one day grow into 1,200 locations.

If that expansion of competition were to occur, it would leave much less of the natural/organic market share for Whole Foods.

Source: Wal-Mart

In addition, Kroger (NYSE:KR) recently became the second-largest seller of organic goods in America with its Simple Truth Organic brand. And just a few months ago, Wal-Mart (NYSE:WMT) -- the company that accounts for one of every four dollars spent on groceries in America -- announced a partnership with Wild Oats organics that promise to offer organic food for rock-bottom prices.

I've already laid out how I think Whole Foods can overcome these obstacles, but it's undeniable that the road forward is filled with far more obstacles than it was just a few years ago.

A still-pricey stock
Despite the fact that Whole Foods' stock has fallen 33% so far this year, many view it as still expensive. In truth, it's hard to price Whole Foods' stock versus the industry.

As you can see, Wal-Mart and Kroger are much lower-priced, but their heady growth days are still ahead. And Sprouts and Natural Grocers have much higher price tags, but they also have smaller footprints than Whole Foods, which means there's more potential room to grow.

Source: E*Trade. Some earnings figures may include non-GAAP numbers.

Perhaps a better proxy would be to look and see that analysts expect Whole Foods to grow earnings by about 14% per year between now and 2017. While that's a healthy number, it's tough to say if a P/E of 25 is warranted. 

The important thing to realize is that Whole Foods has the type of valuation that lends itself to exaggerated moves--both up and down. Should the company's focus on lowering prices of goods take time to filter down to customers, earnings could take a hit in the short-term, and that could send shares lower.

The bottom line on Whole Foods
As I stated above, I'm a big believer in Whole Foods. But it's important to acknowledge the serious headwinds the company is facing in the near-term. How it performs against these headwinds will go a long way in determining which direction the stock moves in the next three to five years--which is the minimum investing horizon we like to use here at the Fool.