A startup company made some very serious accusations against Facebook, that if proven true, could have a wide ranging impact on how advertisers, and even ordinary users, conduct business with the leading social networking site.

Limited Run is claiming that 80 percent of ad clicks received on the Facebook platform are from bots and not real people. As a result, they are pulling all advertisements from the site.

Here is how the company explains the situation:

“A couple months ago, when we were preparing to launch the new Limited Run, we started to experiment with Facebook ads. Unfortunately, while testing their ad system, we noticed some very strange things. Facebook was charging us for clicks, yet we could only verify about 20% of them actually showing up on our site. At first, we thought it was our analytics service. We tried signing up for a handful of other big name companies, and still, we couldn’t verify more than 15-20% of clicks. So we did what any good developers would do. We built our own analytic software. Here’s what we found: on about 80% of the clicks Facebook was charging us for, JavaScript wasn’t on. And if the person clicking the ad doesn’t have JavaScript, it’s very difficult for an analytics service to verify the click.

What’s important here is that in all of our years of experience; only about 1-2% of people coming to us have JavaScript disabled, not 80% like these clicks coming from Facebook. So we did what any good developers would do. We built a page logger. Any time a page was loaded, we’d keep track of it. You know what we found? The 80% of clicks we were paying for were from bots. That’s correct. Bots were loading pages and driving up our advertising costs.”

Limited Run co-founder Tom Mango explained how they used the services of six or seven analytics, including industry leaders such as Click and Google Analytics, before creating their own tool to verify the data. All the outside analytic tools arrive at the same percentage of clicks from Facebook whose origins are suspect as did their own tool.

Visitors from Limited Run’s Facebook ads were not the standard Chrome / Firefox / Safari / IE / iOS users, a strong indication that they might be from web crawlers or bots.

Limited Run initially brought the issue into Facebook’s attention before going public with it. However, Facebook did not offer satisfactory explanation or even bothered to investigate the matter.

“Sadly, Facebook would only reply with automated response about how ‘all analytics services track differently’ when we tried to confront them,” explained Mango.

Mango stressed that Limited Run is not claiming that Facebook is running the bots to jack up the startup’s advertisement cost. He even acknowledged that it could be a denial-of-service attack from a competing business. However, he is disappointed that Facebook did not do more to investigate the matter.

The timing of the report and the attention that comes with could not come at a better time for Limited Run who just launched a beta version of its services just a few weeks ago. Mango claimed that the delay in making their experience public is not for publicity’s sake, but is due to their hectic schedule with the site’s launching. He also cited another incident that served as the last straw, and finally convinced them to post their bad experience with Facebook. He claimed that Facebook charged them $2000 on ads just to change the name of its Facebook business page.

Facebook emailed the following statement to TechCrunch:

“We’re currently investigating their claims. For their issue with the Page name change, there seems to be some sort of miscommunication. We do not charge Pages to have their names changed. Our team is reaching out about this now.”

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