They clutter up the global namespace and are slower to look up than local variables.

First of all, having many global variables is always a bad thing because it's easy to forget you declared a variable somewhere and accidentally re-declare it somewhere else. If your first variable was local then you don't have a problem. If it was global, then it just got overwritten. This gets even worse when you get into implied globals (e.g. when you say someVar = someValue without declaring someVar with the var keyword).

Secondly, global variables take longer for Javascript to find than local variables. The difference in speed isn't huge, but it does exist.

For further reading and a more in-depth explanation of why globals are considered bad practice, you may want to check out this page.