Hmmm. That's strange - no limit that we're aware of. Are you referring to the site domain, something like:
I can't think of why that should cause a problem, unless there was an overlap with the same letters in your Site Title and a replacement messed it up (but we have validation to prevent that).
What did you see in the detailed log (link at the top after cloning, or found in /wp-content/plugins/ns-cloner-site-copier/logs)? We'd be happy to take a look at that if you want to send those to us here:
Did you check the domain field of the wp_blogs table to see if it shows up? Does it show up as a site in your Network admin > Sites list? Did you check the wp_##_options table for the new site to see what the home and site url properties are?
This scenario sounds very strange, let us know if you have any other insights. Thanks!