The free-speech advocacy group said that videos entirely unrelated to Viacom were removed under the order, ranging from independent films to home movies.
It is not the blatant mistakes that the EFF is most concerned about, however. The group believes that many of the videos are likely to fall under the category of 'fair use'.
'Fair use' is a legal concept that allows for the protection of programming such as satire, critique and educational videos from copyright claims.
"If they are making these kinds of blatant mistakes, who can tell how many fair uses of Viacom content they also targeted in their 100,000 takedowns? Hundreds? Thousands?" said the EFF.
YouTube has asked users to report any unwarranted takedowns by way of its own video submission process.
The request for the removal of the videos came after Viacom failed to reach a content deal with YouTube. Viacom is now offering clips from its shows on its own site.
In December, Viacom was among the companies rumoured to be negotiating the establishment of a network-backed 'YouTube killer'.
Viacom did not return a request for comment from vnunet.com.
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