I have no direct experiences with this problem but this is what I will do:
1. Check google index for you domain name (google out: "domain.com") to find any site mentioning my domain
2. Use majesticseo tool if they found anything (also ahrefs)
3. Write this question to google webmaster forum productforums.google.com/d/forum/webmasters
4. Get familiar with google disawov tool

If you are looking for the shitty links they are talking about.

Go back over
Every link package you bought from the wso section
Every fiverr gig you ordered
Every link spam tool you used

Then list all those backlink urls into your WMT. And mark them all "Disavow Please"

You have junk links one way or another. It doesn't matter who you say built the links, a WMT link warning is still there.




C'mon it's only $5, what could go wrong?

Sometimes people do this by accident, or because they've not kept up with the times. I know a web developer who still adds footer links on client's sites.

Try again with the link download. Maybe GWT was having a bad day.

If you want I can take a peek at your site with Majestic. (Shoot me a PM.) Might not tell you anything, because it's often slow and a bit inaccurate, but you can see patterns there.

Check both www and non www version of your site on WMT and you will get backlink data in at least one them. And regarding the manual penalty, you have to download the list of backlinks from all sources - WMT, ahrefs, majesticseo. Then perform a complete backlink audit and anchor text audit. Contact the owners of bad links for link removal. Disavow the links that you couldn't remove and file a reconsideration request to Google.

Go over all your backlinks and delete the ones that are placed in spammy locations.

Try other backlink checkers as well. GWT is known for not showing you all the links.
Even if you didn't order any deals or gigs yourself, someone might have done it for you. A competitor, for example.

Try Linkdox by Link Research Tools is best tool for sorting out unnatural links. If you need any more help just PM.

Sometimes $hit sites link to you even if you did nothing for a year or more. That signals to G00gle that you've only gained crap links and nothing worthy in the last year or so. Same thing happened to me. I just say "give them the special finger" and go on my way with social media and getting real relevant traffic w/o blackhat.
It's like a dam traffic cop giving you a ticket for speeding when you weren't. There really needs to be an objective 3rd legal party so they cannot slap people at will and hurt their business.
Where is the warning ticket?
You can bet someone is developing something like this.