There is a bug in Visual Studio 2005 (but I think I have also seen it in Visual Studio 2003) that causes multiple break points to be set in case you have few files with the same name opened using Script Explorer window. (if you are fortunate enough to have it working).
Steps to reproduce the problem are simple. Just ran a simple page with a Textbox and a Button control and some kind of Validation control. This will ensure that the presence of two "WebResource.axd" JavaScript includes: one for with Validation code and the other one - the standard ASP.NET one. Try to set a breakpoint in the first line of any of the script files included. Use Script Explorer window to get the files. Notice that the breakpoint appears in both files. Also sometimes the focus is moved to one of the other files. Imagine having a couple of scripts included in such a way and all those unneeded breakpoints!
As mentioned above, I have noticed this behavior also in Visual Studio 2003, but I have not tracked it down. I'm almost sure however that there was also the same type of problem also with normal files included in the solution. (yet again, I can't remember for sure).
Fortunately removing breakpoints works correctly so you can remove unnecessary breakpoints once they are created.
As a side note. While writing this article my Script Explorer windows stopped working and this also means that script debugging inside Visual Studio also does not currently work, so I'm unable to provide any more details. I hope though that Microsoft will correct this problem sometime in the future.