1) Possible downtime - Cloud computing makes your small business dependent on the reliability of your Internet connection. When it's offline, you're offline. And even the most reliable cloud computing service providers suffer server outages now and then
2) Security issues - How safe is your data? Cloud computing is Internet computing. So you should not be using cloud computing applications that involve using or storing data that is private and confidential. That being said, established, reliable cloud computing vendors will have the latest, most sophisticated data security systems possible as they want your business and realize that data security is a big concern.
3) Cost - At first glance, a cloud computing application may appear to be a lot cheaper than a particular software solution installed and run in-house, but you need to be sure that cloud application have all the features that the software does and if not, are the missing features important to you?
4) Inflexibility - Be careful when you're choosing a cloud computing vendor that you're not locking your business into using their proprietary applications or formats.
5) Lack of support - Customer service for Web apps leaves a lot to be desired -- All too many cloud-based apps make it difficult to get customer service promptly – or at all. Sending an email and hoping for a response within 48 hours is not an acceptable way for most of us to run a business".