But Google penalties often scale along with other factors, so if there's a problem with the natural search ranks of a large web entity, chances are it's not a small one. Many troublesome Google penalty issues arise because automation protocols did not take search compliance into consideration. Systems are designed for the convenience of the users. But if search compliance was not considered during development, the automation itself can be the culprit.
The two most common Google penalty related automation issues involve the inadvertent creation of redundancies at the content and domain level, and filename redundancies across multiple directories.
For example, the null set redundancy exists when a page gets created even when there is no data. If more than one empty page is created, you have pages that are redundant by virtue of having no data - perhaps only header, footer, and nav. Create enough of these pages, and it can trigger a Google penalty because it can appear to be a deceptive strategy by virtue of the numbers.
Sometimes the implementation choices themselves lead to Google penalty issues. We know that Google can have problems with dynamic sites if the developers chose to mask the filenames without including the extensions. We have many examples of sites going intermittent with their ranks once they reach a threshold size. This is one case where critical mass works against big sites.
Even though there are a good number of high level seo pros we respect, there are very few who have the kind of experience our team has with Google penalty issues on large/multiple sites. re1y.com's contributors include some of the most successful enterprise level seos, including owner Bob Sakayama, Google penalty expert. Bob is heavily involved with this site and shares his experiences both with actual penalties and preemptive strategies starting with this overview.
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