This is probably obvious to any reader here and I believe Google has said this in the past, but Gary Illyes from Google confirmed it is very possible a site can be impacted by both a manual action and algorithmic issue.
Gary said on Twitter, "it's certainly possible a site is affected by penguin and also has a manual action for links related issues."
Here is the set of Tweets:
@fbotha1 yes, it's certainly possible a site is affected by penguin and also has a manual action for links related issues.— Gary Illyes (@methode) October 15, 2015
Honestly, it is probably not that uncommon to have a manual action for link schemes and also be impacted by Penguin. I once asked Google was is the percentage of overlap, but they didn't have the number to give me immediately and I guess they didn't want to look it up or share it with me. I wouldn't be surprised if there wasn't a 25% overlap or more.
Forum discussion at Twitter.