The way JavaScript works is: - The web page points to a JavaScript program. - Your browser transparently downloads that JavaScript program, temporarily installing it into the browser. - Your browser executes the JavaScript program where the web page specifies it should.
JavaScript code gets executed on your computer, not on a remote server.[0] So in effect, the GNU AGPL is exactly the same as the GNU GPL for these programs. Now, for your actual question: the various JavaScript files are generally several different programs that just happen to be loaded by the same web page. It's basically the same situation as having several different programs installed in your OS: a bunch of unrelated programs are perfectly able to coexist on the same computer, regardless of license restrictions. For example, software under version 2 of the Apache License can be on the same system as software under version 2 of the GNU GPL (see Android, for example; the kernel Linux is under the GPLv2, while much of Android's userland is under the Apache License version 2). Similarly, if a web page uses one JavaScript program under the AGPL, that doesn't mean that some other JavaScript program it loads is also under the AGPL. [0] There is such a thing as JavaScript code being server-side, but I don't think it's very common.
