When you're thinking of investing in an aerospace and defense stock, there's one name that comes immediately to mind: Boeing (NYSE:BA).

At first glance, Boeing stock seems to "have it all." It's big -- the biggest plane producer on the planet, with $88.4 billion in trailing sales . It's diversified, with operations in all three of the industry's major arms -- air, space, and defense. And to top it all off, Boeing stock has outperformed the S&P 500 index of companies over the past year.

And yet, for all the pluses surrounding Boeing stock, the company has a few minuses as well -- minuses that in time, could begin pulling its stock price back down to earth. Here are three of them.

Boeing's 787 Dreamliner could be the future of Boeing -- but do mind the smoke alarm. Photo: Boeing.

Dreamliner still a nightmare
Boeing's 787 Dreamliner passenger aircraft is a marvel of technology, featuring  21st Century composite materials, fuel-efficient engines, advanced fly by-wire controls, and bright LED lighting and larger windows for passenger comfort. There's just one downside to the plane...

From time to time, it catches on fire.

Actually, no. Come to think of it, while the occasional onboard bonfire is the most high-profile problem the 787 has experienced, the new aircraft has experienced a few other bumps in the road to widespread adoption. Over the past couple years, reports have filtered in of electrical problems in auxiliary flight systems aboard 787s operated by Qatar Air and United Air Lines (NASDAQ:UAL), oil leaks and cracks in windows and engine casings at All Nippon Airways.

For a time, it seemed like customer complaints were dying down. But then, just last week, we learned that one of the two engines powering a Thomson Airways 787 en route from the Dominican Republic to England abruptly stopped working -- while the plane was hung out over the middle of Atlantic Ocean. It took four hours of nerve-wracking flight on only one engine, over open water, before the plane could be brought to rest -- safely -- at a Portuguese military base in the Azores.

An isolated incident, after a mostly uneventful year for Boeing's 787, you say? Perhaps. But one passenger comment following the crisis sums up the risk to Boeing's 787 franchise: "We will not be flying on that plane again," Caroline Barton said.

The Boeing F/A18 Super Hornet, flying CAP. Photo: Boeing.

Losing all the big fighter contracts
Selling for as much as $298 million a pop  (at list prices), the 787 business is a very big deal to Boeing. But even more important to the company is its defense business, which according to S&P Capital IQ figures brings in nearly $25 billion in revenues for Boeing annually.

Or rather, it used to bring in that much. After more than five years of war-fueled spending increases at the Pentagon, last year was the first year that Boeing saw revenues decline for its military aircraft and related global services and support divisions. But "last year" won't be the last year we see this trend hurt Boeing.

This is a bigger story than just the one about how the U.S. Congress is cutting defense spending. Boeing has also begun missing opportunities to diversify its defense business away from America. In recent years, Boeing has suffered a string of hi-profile defeats on bids to sell its fighter jets to foreign militaries:

Now don't take this to mean that Boeing's entire defense business is going to disappear in a flash (and a bang). It won't. With billions of dollars' worth of revenues coming in from military helicopters, troop transports, spyplanes, bombs and rockets, Boeing's going to be a force to contend with in the defense biz for years to come. For the time being, it's only in fighter jets where the company is losing the dogfight -- but even that might be enough to bring Boeing's stock price down a tad.

Boeing's KC-46A aerial refueling tanker in action. Source: Boeing.

Even when it wins, it sometimes loses
Perversely, the third problem (and the last one we'll be talking about today) with Boeing's stock is that even when it wins military contracts, Boeing sometimes loses. This was the case with the company's "victory" in the contest to build the U.S. Air Force's KC-46A refueling tanker three years ago.

As you may recall, Boeing fought a heated contest, and waged a pretty nasty PR war against rivals Northrop Grumman (NYSE:NOC) and Airbus (NASDAQOTH:EADSY), for the right to build the KC-46A. Boeing ultimately emerged victorious with a bid to provide the Air Force with 179 planes for $31.5 billion.

Problem was, Boeing's final bid to win the business was (in the words of Airbus North America Chairman Ralph Crosby) "very, very, very aggressive." The Air Force, after all, had been prepared to pay as much as $35 billion for these planes. So right from the get-go, Boeing dug itself a $3.5 billion hole in hopes of striking gold with the Air Force contract. That made it difficult for Boeing to earn a profit from the program -- and as we've since learned, Boeing's problems have only gotten bigger over time.

Last quarter, Boeing warned investors that problems with the wiring of its KC-46A's necessitated taking a $272 million charge to earnings in Q2 2014. This announcement followed the revelation last summer that cost overruns had already pushed the KC-46A program $700 million overbudget -- and as a fixed-cost program, these are cost overruns that Boeing will need to absorb itself.

Foolish takeaway
So let's sum it all up for you: In Boeing stock we have the opportunity to own both arguably the world's most successful aerospace and defense company -- but we also have a company with significant "issues" to its business. On the one hand, the company's rolling in revenues, and doing 10% more business in a year than its archrival Airbus can manage. On the other hand, though, significant problems with some of its highest profile programs are beginning to nibble away at the profitability of those revenues -- and pushing Boeing's net profit margin down below 6%.

Are these problems significant enough to cause Boeing's stock price to lag the market going forward? Time will answer that question for us. For now, all we want to do is make sure you're aware that the problems are there.

Caveat investor.