John Mueller replied to a webmaster with an interesting issue recently. They kept a dev site as a subdomain of their main site. As The SEM Post describes, the subdomain was indexed and then "spammed via a CMS exploit." The manual action was eventually sent to the main site. Mueller's response:

"If the manual action was specific to the subdomain, then that wouldn't - from a manual actions point of view - have an effect on the rest of your site. If you've taken care to remove all of that, then after a reconsideration request things should be fine."

He also suggested that blocking the indexing of the dev site would be a smart move. Since this was a dev site, it might be a very specific situation. I wonder how much these are looked at on a case by case basis? Have you ever seen a manual action on a subdomain have no impact on a main domain? The SEM Post presents the interesting example of Blogger, which uses subdomains for different users. If one of those users produced spam, it would impact all of Blogger - which doesn't seem to be the case.