Most developers prefer to seperate design from functionality. This is a noble goal, but sometimes hard to implement. In my experience developing web applications, the most typical collision between design and functionality happens in JavaServer Pages, the most typical templating format of web front-ends in Java web applications. Most readers know JSP's, but for those who don't, think of it as Java's PHP, or the templates we use for producing HTML.
However, a problem which is still at large in web applications today is that these templates are designed by Java developers, or pure programmers with little knowledge of web design and web standards. Or worse, programmers that believe they do know web stuff when they actually don't, or don't know how important the web front-end really is.
The problem with programmers doing these JSP's is that that they are doing design, sometimes even when they don't have to. The classical example of this is putting layout of the entire page in<>'s because they can't handle CSS. Tables are even used for lists. They embed JavasScript and styles in the HTML. If they do use CSS, they might inconsistently use classes and id's.
And by the end of the day, the result of the programmer's futile attempts at doing web design ends up plain ugly.
Then to the rescue: The web designer.
What follows are several strenuous days of the programmer picking at the JSP, trying to make the web design fit and look like the web designer's example.
There are two ways to avoid this pattern. The first one is: Programmers, steer clear of web design. Just leave the design till later on. Learn the basic DOM-elements of HTML you will be producing, and use it in a consistent way.
But remember that no matter how well the programmer uses div's and id's in the most elegant scheme of definitions, the web designer will definitely come up with his/her own ones that must be complied with across all the JSPs in an application (and there are often quite a few of these, mind).
Needless to say, the interests and motivations of a designer are very far from those of an innate programmer. I think one could even draw the conclusion that these two professions draw quite opposite personality types. Perhaps this is also why we often detest the products of eachother.
Me, as a programmer for instance, I hate doing web design. I can never figure out a set of good colors that work. I can't get CSS stuff working, it's just stuff bouncing around. And personally, I'm a functional person, not esthetical. I can't see the point of improving design once you have achieved usability, although I do of course recognize that there is an actual need for this in attracting use and success of an application. What more, I envy this effect that often leaves the designers being the heroes of a successful web application as they make the outlook, the good looks, the bells and whistles.
Good architecture and good programming goes unnoticed (meaning that it only gets noticed when it's done badly). Yes, I am jealous :)
Still, spite the gap between our personas, I have seen programmers successfully venturing into the world of web design, as well as designers learning the skills and becoming adapt programmers. Some have even been doing both since they started of with their own LAMP application and had no way of outsourcing design nor programming. These are programming designers. I believe that EVERY web application project should bring one of these on board.
I would also like to note that inversion of design/design injection can be done with SiteMesh, which is a great tool for templating and page modularization. This is a good way of giving the programming designer a file/decorator/template where he or she can work freely while not interefering with the tangles of the programmers.