Some limitations of Selenium Automation tool are as follows:
It does not support and non web-based applications, it only supports web based applications.
Its an open source tool so in case of any technical issues you need to rely on the selenium community forums to get your issue resolved.
You need to know at least one of the supported language very well in order to automate your application successfully.
No inbuilt reporting capability so you need plugins like JUnit and TestNG for test reports.
Lot of challenges with IE browser.