There is no standard for instant messaging systems, the people you want to instant message must use the same instant messaging system. This forces many people to end up downloading and using many different kind of instant messaging systems to be able to talk to all of their friends from the various systems. 
This leads to confusion and frustration. 
Security can also be a big problem. Instant messaging exposes systems to hackers and viruses..See Regulatory Concerns... 
Instant messaging also has the potential of becoming a distraction in businesses. Instant Messaging: Valuable tool or distraction? Computer World, July 13, 1999 
Like the Macintosh and the Internet before it, instant messaging technology is sneaking in the back door of corporate America, presenting IT departments with new opportunities and new challenges. An exclusive Computer World survey of 149 information technology managers found that 17 percent are aware of some instant messaging use in their companies but that most don't provide technical support for it. And 78 percent of the IT managers said instant messaging is unnecessary because existing e-mail and groupware work fine. Another worry: Employees may waste time on private chat sessions. The most popular instant messaging tool is America Online Inc.'s Instant Messenger, a free piece of software that lets users see which friends or colleagues are online. They can send a message that immediately pops up on the addressee's screen, and two or more users can have an interactive discussion. Today, about a half dozen workers use Instant Messenger for personal communications and for giving technical support, Soper said. He said the technology may become a valuable business tool in the future. But Nelson said he's still trying to figure out "whether it's a valuable business tool, or whether it has the potential to be a distraction" ...Full Computer World Story... 
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