1. Complex code usually contains some horrible callback spaghetti, which is not pleasant to debug at all.
2. General flakiness, or, as I call it, the "WTF happened?" syndrome. I run into this all the time. Change or add something - suddenly you find the web page broken. Okay, so there's a bug somewhere. Click developer tools - console... blank. No error messages, nothing. Just you and the broken web page. Just the other day I was trying to integrate a select2 input field into some angular.js-powered page and ran into all kinds of weird issues. But why does it even have to be a problem? Why can't I just stick a new control into a web page with a click and maybe a few lines of code? Hey, remember those things called "Visual Basic" and "Delphi"? UI programming with these was a blast, all the controls looked and behaved the same across all applications. And then there was ActiveX. The idea behind ActiveX is almost futuristic compared to the shit we have to put up with.
3. Type system. Made a typo in a variable name? Bad luck, Javascript will introduce a new variable and you'll have fun chasing a non-existing bug. Oh, look, here's a function: "function foo(param)". I wonder what does it do? Unfortunately, the previous maintainer has not left much comments, so now I have to dig through the implementation to find out what the parameter should be and what values the function may return.
These are my main issues with javascript. I hope sometime in the future we'll throw out the whole Javascript/HTML thing and start writing web application front-ends in a language that is more geared towards UI programming. I can imagine having a nice declarative language (instead of HTML) to describe what the interface looks like, and a statically typed imperative scripting language to describe UI behavior. It would also be awesome if these technologies allow for painless integration of independent UI components (a bit like ActiveX controls). But those are just dreams...