The presentation layer developers get into lot of trouble when they work on a web based application. After the advent of dynamic presentation layer technologies (such as JSP, RHTML, ASP etc) HTML components and the language code gets nested with each other. Usually after some time the code becomes messy particularly if you dont have separate code for every layer in the page. But however loosely coupled your code is, the resulting page may not be what you expected and most likely you will miss something not appearing or not appearing the way you want.
I have seen developers trying to probe their dynamic code and trying to locate the problem. But a best place to start would be from your browser and view the source code generated. Here is the reason why. However complex your system is and whatever be the technology that you use for the server side application, everything has to ultimately get transformed into one single HTML file that comes to the browser. So it is better that you study the resulting HTML layout of your program(s). Most of the time you know which part of the HTML is causing the problem, and you would definitely know which program/code generates that section of the HTML.