I tried to see the list of classes inside a package in an android application using AndBug command 'classes com.package.name.example'.
The output shows only one class file.
But when I decompile the apk using dex2jar and view the classes inside the package com.package.name.example using JD-GUI, I can see two class files.
The class file that I want to trace is not being shown in AndBug, while it is shown in JD-GUI.
What could be the possible issue?
It's very likely a bug with AndBug. You should at least submit an issue to the project page along with a dex file, if possible, so that they can reproduce the issue: https://github.com/swdunlop/AndBug/issues
For bonus points, debug the issue yourself and submit a pull request. :D
There are always bugs with disassemblers and decompilers. Some people intentionally find and exploit them to prevent others from reversing their applications.