Cloned site pointing to original site's database - can this cause problems?
The only way this could cause problems would be if the filesystem became out of sync. Since you didn't create, edit, or delete any content, this shouldn't be the case. If you have anything running on a cron hook which creates files you may see 404s in your logs. An example of this would be something like boost or advagg which create cached html/css in the files dir. Even if this is the case however you will be fine once cron has run again from the live codebase.