We get something similar in eclipse when the project committed to the repository defines the build path.
If the local machine (that pulled the repo) doesn't have classes.jar and squak_device.jar (for eclipse). This is configured
In eclipse these changes are made by right clicking the project and selecting Build Path > Configure Build Path.
Then from the Libraries tab, edit the two jar file locations.
I pulled up Netbeans, and it looks like you should have a similar type of configuration for each project.
Right click on the project, and go to Properties
My guess would be to check the paths for the "Java Sources Classpath" category.
You can set up your git ignore file to prevent these local configuration files from being included in the git repository. Unfortunately I don't know which file(s) need to be ignored for a netbeans project. If you don't ignore them though, each time someone pushes their changes, they will likely overwrite the version of the file in the repo with the setting changes they made locally (breaking compilation on other clients whose file locations differ).