The error you get is most probably the result of a custom control that cannot be indexed, thus breaking all the whole process.
You can have custom controls on your pages, however if any of the controls contain code which somehow messes up with search engine indexation you may experience errors like this one.
Have you tried to create a new website from the Project Manager and add some of the default controls and then index it? Can you run such a test and check if the error still shows up. If the problem comes from a custom control you need to escape the crawler request. Please refer to the following code sample:
if (this.Page.Items["IsInIndexMode"] == null)
// your logic here.
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