There are two different threads at Google Webmaster Help where sites with Google manual actions received responses back from Google citing bad link examples including links already in the site's disavow file.
As you can imagine, this can be very confusing for webmasters. The webmaster disavowed the bad links, then Google tells the webmaster his site still has a penalty because of the links he already disavowed.
Read what this one webmaster said:
I looked at the links which were given as sample URL's from Google on the latest rejection and it is in my disavow file which was uploaded a week prior to my reconsideration request. Is this an error from Google as I am assuming that Google will be bombarded by these and some errors might come through the net, if so should i just reconsider straight away saying, the links you have given I dispute as they are already disavowed and I don't understand what else I need to do?
Another webmaster wrote, "The above URL's have all been disavowed at a domain level in the most recent disavow file uploaded. Given this, how is then that these URL's are still being flagged?"
Yea, that is confusion 101.
This is somewhat related to our story named Google's Link Report Now Much More Representative Of Your Links To Your Site. Where Google improved their link report because the example URLs provided were not enough.
But here, this is a way more confusing situation for webmasters. They disavow links and then Google tells them they have a manual penalty even with the links disavowed.