Most everyone would agree that the drug business carries some unique challenges. Isolating disease targets, developing formulations, designing and running clinical trials, meeting regulatory requirements -- all of these tasks require an enormous investment of time and expertise. Still, once a drug has jumped through these various hoops and landed on the market, pharmaceutical companies can usually take comfort in the fact that on the technical side, things are mostly on autopilot. At that point all that's left is for their manufacturing facilities to pump out the pills for the public and for their sales and marketing departments to sell them.

Unfortunately, things don't always go so smoothly, as GlaxoSmithKline (NYSE:GSK) is now discovering. The pharmaceutical manufacturer disclosed on Friday that the Food and Drug Administration halted distribution of two of its drugs: the depression treatment Paxil CR and the diabetes medicine Avandamet. The FDA had apparently warned Glaxo to fix problems that were causing these tablets to split. In the case of Paxil CR, one piece may contain the actual medication and the other may hold the inert buffering substance. For Avandamet, a combination of the medicines Avandia and metaforin, the FDA claimed that Glaxo could not guarantee the potency of the Avandia portion in the case of split pills.

Glaxo was quick to add that it does not believe the problems represent a health risk and that it is fine for patients to continue to take the pills they have. Despite the lack of safety problems, the firm's market share may be hurt. If a shortage develops and lingers, chances are that patients will switch to competing drugs. Avandamet has relatively small sales, but Paxil CR had $725 million in sales last year and is used by 450,000 people in the U.S., according to TheNew York Times.

Admittedly, Glaxo is not the first drug maker to run afoul of regulators on manufacturing compliance. The most recent high profile case involved Chiron (NASDAQ:CHIR) and the flu vaccine debacle, but Schering-Plough (NYSE:SGP), Eli Lilly (NYSE:LLY), and Abbott Laboratories (NYSE:ABT) have all had their run-ins with the FDA over production facilities. It can be a costly experience. This history makes the fact that Glaxo let its problems with the regulatory body fester all the more puzzling.

Glaxo indicated that it is working with the FDA to resolve the issues. Investors can only hope that the FDA is in a forgiving mood.

Fool contributor Brian Gorman is a freelance writer in Chicago. He does not own shares of any companies mentioned in this article.