The most common gotcha I encounter in Javascript has to do with callbacks. I see this problem all the time in my own code and that of my colleagues: callbacks that have been registered either more or less times than the author of the code expected. Usually more times.
This can manifest itself in many ways. Usually in the form of a UI element being displayed more than once, but often more subtly such as a HTTP request being sent more than once. Often the bugs only manifest themselves after a certain sequence of actions, for example: click this UI element, check this radio box, then hit submit and watch the net tab.
It's so often the root cause of Javascript bugs that if I or somebody else on my team has a Javascript problem, I often start by asking myself if it looks like it could be this. Lately I have begun to wonder if there isn't some slight truth to that inflammatory "Callbacks are the new goto" story that was on here a couple of months ago [1].