If you are using the same library jar files with source attachements in different NetBeans projects, it could happen to you that breakpoints you set in one project magically appear in an other project, too. Unfortunately they are not deletable there, only in the project where they were set originally.
Often I have to switch between many projects back and forth. Then getting rid of these “ghost” breakpoints proved difficult. Here is what to do:
On windows, NetBeans stores workspace configuration data in your windows home directory under
AppData/Roaming/NetBeans/version-number. In subdirectory
config/Services is the file “org-netbeans-modules-debugger-Settings.properties” located. Breakpoints are stored in this file. After deleting them there, you definitely get rid of them!