You'll have to describe your situation in much more detail. I've been using Appium for a very long time, and I've never seen fragments be an issue.
To start, you can list what version of Appium you're using, some Appium logs (use a pastebin service. Please don't spam the forum), and a sample of your testing code that demonstrates the issue. What is the layout structure of your application?
What does the Android SDK uiautomatorviewer tool say for your application? Ideally, you would make a post with the XML .uix file and screenshot .png file attached so everyone can take a look at your app.