MySQL server crashes whenever a container reaches its quota

I have dealt with this issue multiple times. When a container (virtualserver) reaches its quota limit, MySQL crashes and will not restart until that issues is resolved. This crashes MySQL for ALL containers on that server. Is there a way to resolve this and make a quota limit NOT crash MySQL. My Assumption is that the hard limit includes mysql database size. Can we remove or change the limits independently? Its quite difficult when a customer calls and says their website is down and we find its because some other user uploaded too many files.