Image Maps are a popular way of allowing the visitor to get an overview of a website in a graphical form. Image maps consist of an image that by allowing users to click on different parts, guide the user to different sections of a website. These can confuse web spiders, which might not be able to parse the image map, making it impossible to extract the links contained within.
Incorrect HTML codeAs HTML is a fairly easy language to learn and use, however quite a proportion of web pages contain invalid HTML code, this can confuse web spiders and cause any page that contains invalid code to be indexed incorrectly.
Dynamic Web PagesA large percentage of websites today use dynamic webpages comprised of pages that are built using a 'back-end' database, with pages created "on the fly". These should generally be avoided as dynamic pages are often not available to be indexed by web crawlers every time they visit a web site. For example Google does not crawl any URL which contains the "/cgi-bin/" within it.
Beware of splash screens. When a website is visited by a search engine crawler, most attempt to start indexing the page, looking for text to store and hypertext links to follow. However most cannot parse graphics welcoming human visitors to the site and will abandon attempting to index past splash screens.