Sort itself out
Definition 1 of 2
Pro Tip 1/3Time Dependent
The phrase implies an issue will resolve after some time without anyone's intervention. 
I know you're upset about the disagreement, but it'll sort itself out soon.
Pro Tip 2/3Optimism
Conveys a hopeful belief that a situation will improve naturally. 
The confusion about the new software will sort itself out as we practice.
Pro Tip 3/3Casual Assurance
Used informally to reassure someone without making specific promises. 
Your lost luggage will likely sort itself out once the airline tracks it.