JDeveloper Clean All command does not appear to be deleting contents of classes folder, this can lead to issues as you may be referencing old class (class file may have been refactored to other package). In this blog entry, i would describe steps to create external tool to delete classes folder. I will describe two options, 1) using cmd.exe and 2) using ant build file.
External tool (cmd.exe) to delete classes folder
External tool (ant build file) to delete classes folder