Most collaborative designs are infested with regular conflicts, as evident from those between differing goals and methods of web site designs. A few of the ongoing ones follow.

Lack of Collaboration in Design

Earlier stages of the web did not enjoy as much collaboration between web designs and larger advertising, campaigns, customer transactions, social networking, intranets and extranets as there is now. Web pages were mainly static online brochures disconnected from the larger projects.

Even today many web pages are disconnected from larger projects. Special design considerations are necessary for use within these larger projects. These design considerations are often overlooked, especially in cases where there is a lack of leadership,understanding or concern for the larger project to facilitate collaboration, often leading to unhealthy competition or compromise between departments, and less than maximum use of web pages.

Liquid versus Fixed Layouts

Early 1990s saw programmers as the original web page designers. Present designers come from a graphic artist background in print, with absolute control over the size and dimensions of all aspects of the design. On the web however, the Web designer has no control over several factors, including the size of the browser window and the size and characteristics of available fonts.
To compensate for this many designers wrap their entire webpage in a fixed width box, limiting it to a fixed layout. Some create the illusion of liquidity by building the graphics for their webpage at a size larger than any current standard monitor size. Other designers oppose this as it ignores the preferences of the user. They propose a liquid layout, where the size of the Web page adjusts itself to the size of the browser window. Many prefer to set a standard browser size like 1024x728 and the website be viewed with the said browser setting.

Abode Flash

Many graphic artists use Flash because it gives them exact control over every part of the design, and anything can be animated and generally "jazzed up". Flash detractors claim that Flash websites tend to be poorly designed, and often use confusing and non-standard user-interfaces. The vast majority of Flash websites are not disability accessible (for screen readers, for example) or Section 508 compliant. Another issue is that sites which commonly use alternate content for search engines to their visitors are usually judged to be spamming search engines and are automatically banned.

The latest incarnation of Flash's scripting language, called actionscript, respect the browser's font size and allow blind users to use screen readers. Actionscript 2.0 allows the use of CSS, XML, and the design of class-based web applications.

Section 508 of the Rehabilitation Act of 1973, is a law requiring that electronic and information technology be accessible to persons with disabilities. A screen reader is a software application that attempts to identify and interpret what is being displayed on the screen. This interpretation is then represented to the user with text to speech, sound icons,  or a braille output..

CSS versus Tables

When Navigator 4 dominated the browser market designers used to lay out a Web page by using tables. Even simple designs for a page  required dozens of tables nested in each other. But afterwards  designers started turning toward CSS as an alternate, better means of laying out their pages. Today, all modern Web browsers support CSS with different degrees of limitations..

The main drawback with CSS is that by relying on it exclusively, control is essentially relinquished as each browser has its own quirks which result in a slightly different page display. This is especially a problem as not every browser supports the same subset of CSS rules. Designers, familiar with table-based layouts find CSS design rather cumbersome
Most modern browsers have solved most of these quirks in CSS rendering and this has made many different CSS layouts possible. Some people still use old browsers,  eg Internet Explorer 5 and 5.5

Conflict Between Looks and  Works

Web developers and search engine optimisation consultants (SEOs) often end up in disputes over looks and works of a page.While the designer wants more pretty graphics, the SEO prefers lots of  keyword-rich text, bullet lists, and text links. Some may rely more on advertising than search engines to attract visitors to the site. But the SEOs obsess about how well a web site works technically and textually: how much traffic it generates via search engines, and how many sales it makes, assuming looks don't contribute to the sales. There is a possibility that a web design may integrate the two disciplines for a collaborative and synergistic solution because how well a site works, may depend on the graphic designer’s visual communication ideas as well as the SEO considerations.