GnuCash may be configured to be strict about double entry, or you may configure it to be "loose."
In "loose" mode, you can create unbalanced transactions, that is, transactions where the "splits" don't balance to zero. That discards the validation that comes from using the more strict double entry scheme, which is probably not a really wise move. In effect:
If you aren't sure of what you're doing, you likely do not want to discard the validation of double entry, as this helps you keep your accounts balanced even when you're not perfectly clear on this.
If you are an accounting whiz, you'll know that it's really important to keep things in balance, and again will prefer double entry.
But if you decide to "outsmart the system," and have a number of unbalanced transactions, you'll probably want to clean this up at some point. To clean up these unbalanced transactions, you Scrub the account clean by choosing Scrub from the window menu.
The process will examine each transaction; if the transaction doesn't balance, a split entry will be created and placed into an account named Unbalanced. You may then review these splits and move them to their proper accounts.
Warning: Functionality Changing...
At present, control over whether GnuCash is "strict" or "loose" is established at compile time, and defaults to strict.
In the future, there will be no option of "looseness."