Hi Greg - short answer is, it depends... Which means, of course, there's a long answer
In Google's eyes, subdomains are often, though not always, treated as separate entities from the main domain, meaning if content or issues on them is giving Google trouble, that won't necessarily extend to the other parts of the domain. However, this isn't always the case. We've certainly seen times when having spam or manipulative behavior on a subdomain meant the root domain and content on it suffered as well.
In the case you're describing, if the crawl issues are things like missing meta descriptions or long titles or other less-than-critical errors, I wouldn't be too worried. But if it's lots of 404s or duplicate content or infinite redirect loops, those could cause issues.
If you're really not worried at all about what Google thinks of the subdomains or the content on them, you could always use robots.txt to block them from accessing it, which should cause Google to not weight that content when judging the site as a whole.