It is amazing how easily the processing of samples can lead to contamination of data. Something like 22% of sequenced genomes contain AluY elements from the human genome. As noted in the following posting from The Scientist, this alarming discovery could also be indicative of contamination of sequenced genomes by DNA from other sources, such as the commonly used E. coli, which could be problematic when working with other bacterial genomes. This possibility could have grave consequences when it comes to evaluating horizontal gene transfer.

http://www.the-scientist.com/news/display/57990/

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016410

Though, it should be noted that as per the article in The Scientist, this is only applicable to female scientists (“But probably the most common contaminant is the scientist herself.” from paragraph 4).