Overall, although cell lines can have genomic problems they can still be used to provide important information about molecular interactions and inductions. In addition, they are a fantastic resource for researchers who do not have the stomach for animal research. Contamination is bad. It comes in many forms, and results, in all cases, from growth of organisms other than your cells of choice, in your culture vessel. Contamination usually involves fungi, bacteria, or micoplasma.
Fungi make fuzzy mats and put out long fibrous processes.
Micoplasma are strange organisms that live within cells, and are only now being implicated in human disease. Our laminar flow hood is designed to keep out these types of critter. Another way to mix your cells is to pipette them too far up into your pipettor more than once, in one day. Even within the hood, care should be taken to avoid contamination. If at all possible, avoid sitting down the lids of bottles or cultures.