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Hi there! Out of curiosity, when you say that pages are being marked as spam, do you mean they're being given a spam score? And what is that score?

Hi Jeeyaul, As long as the links pointing at the 2nd and 3rd level pages (and the site in general) are good quality, then I wouldn't worry about this too much. I certainly don't think it's bad for rankings and is actually more likely to help those 2nd and 3rd level pages rank better. If, on the other hand, these links aren't great quality or could be seen as manipulative by Google, then that could be bad for rankings. You could take a look at this blog post that I wrote late last year which talks about what makes a good and bad link: https://moz.com/blog/the-anatomy-of-a-link I hope that helps! Paddy