Bitter divorces aside, taking your partner to court is rarely the best way to settle things. Unfortunately, Amylin Pharmaceuticals (Nasdaq: AMLN) doesn't seem to have much other choice.

The biotech is partnered with Eli Lilly (NYSE: LLY) to sell diabetes drug Byetta and an upcoming extended-release version called Bydureon. Amylin doesn't want to stop working with its big pharma partner, but it doesn't want Lilly's sales force doing double duty, either.

Lilly recently established a partnership with German Boehringer Ingelheim to develop multiple diabetes drugs, the first of which, Tradjenta, was approved this month. Lilly apparently plans to have one sales force marketing both drugs, which Amylin isn't too happy about. Amylin says it tried to resolve the issue amicably but was forced to go to court because the two couldn't work out their differences.

Amylin claims Byetta and Tradjenta are competitors, but that's stretching the definition just a bit. Tradjenta is an oral medication in the same class as Merck's (NYSE: MRK) Januvia and Onglyza from Bristol-Myers Squibb (NYSE: BMY) and AstraZeneca (NYSE: AZN). It'll be used early in the progression of diabetes, while Byetta is typically used after diabetics have failed oral medications since it has to be injected twice daily. Bydureon, which is only injected once a week, might have a better chance at grabbing those early patients.

The bigger issue for Amylin is likely how much effort the sales force will put into each drug. Lilly is likely more concerned with getting shiny new Tradjenta off to a good start -- competition with megablockbuster Januvia is going to be tough -- than tired old Byetta and its slipping sales.

Investors aren't privy to the partnership documents, so it's hard to know how this will end.

Fighting with the company you're supposed to be working with isn't exactly the best way to grow sales, so investors should hope it comes to an end quickly.

Keep track of Amylin and Eli Lilly as they fight it out in court. Click on their names to add them to My Watchlist, which will help you keep track of all our Foolish analysis on the companies.

Motley Fool Rule Breakers is always on the hunt for hot drug stocks and other cutting-edge picks. Click here to see all of our latest discoveries with a free 30-day trial subscription.

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Motley Fool has a disclosure policy.