The way I understand it...
There is a blacklist of domains maintained by HubPages. Additional sites can be added to this blacklist by the HubPages team if a hub is flagged with a link to a potentially offending site. But let's assume that you're talking about a site that's already blacklisted.
When you publish a Hub, a script scans all of the links in your Hub. If any links point to a blacklisted domain, they're flagged as "Links to Prohibited Sites." When you have a violation, it will be listed at the top of your hub.
There should be an arrow next to it or something you can click on. That will expand the statement of the violation and tell you specifically which links / URLs are prohibited. You'll need to remove those before your hub can be clear of violations.
It happened to me once, and I don't remember all the details, but I do remember that I could see the specific URL at the top my Hub in the violations section. I removed the URLs, and no more violations.
There are a lot of reasons for why a site can end up on that blacklist, so that's a tougher question to answer. I think there's a list in the Terms of Services.