There are a lot of things that website owners are currently doing and they might not even be aware of the fact that their SEO rankings are being hurt and negatively affected.
Too Many Reciprocal Links
For those website owners who have just started out, having a couple dozen reciprocal links is alright. On the other hand, going overboard gives the impression that someone is merely linking to positively affect their ranking, making it look like a black hat SEO tactic.
Duplicate content on a website is not linked by Google. Search engine robots need to be notified if duplicate content needs to be placed in different places on a website for the visitors, to allow that content to be linked.
Another factor that can be cause a problem for SEO rankings is when versions of the same homepage are linked multiple times. Whenever linking back a website it should be made sure that that only a single URL is chosen and used further on. There is no doubt that visitors will be directed to the same place is two or more different URL structures for a main page are accidentally linked, but the capabilities of the link are then being spread out. Ultimately merely a single one canonical URL associated with a website is chosen by search engines as well.
As mentioned, choosing a single URL and sticking to it is the best thing that can be done in such a case. Making a 301 redirect on URLs that have been used in the past or have been linked to is another appropriate option, allowing them to redirect to the main URL that has to be used. Thus search engines are able to identify the main URL of a website and the complete capabilities of the link are focused where they should be going.
Search engines are unable to crawl a website properly if flash is being used. SEO efforts and ranking can be drastically affected if a flash intro is being used. It cannot be doubted that attracting traffic to a website is much more ideal than having flash intros.
Lack of Content
When identifying what a website is about, text is required by search engines, therefore a webpage made up mostly of images will not rank well. Search engines can easily get confused of what to do with a webpage if it does not have an adequate amount of content. The effective use of keywords and in fact having keywords actually present in the content, are also part of this aspect.
Problems can also be caused by broken links whether they are present on the site in question or another website that is redirecting visitors to a specific site. Depending on the strength of a reciprocal link, SEO ranking can also be affected if a high PR webpage that was redirecting potential visitors to the target website suddenly disappears.
Thus keeping these factors in mind can ensure that the SEO ranking is not negatively affected.