If your employees have accrued some hours on a benefit, say Vacation or Sick Time, Core tracks the time entries as well as the benefit usage logged against the benefit when computing the hours used from it. For example, if an employee logs 8 hours against the Vacation Time activity (specified in Global Settings > Master Information) and adds a benefit usage of 16 hours against a benefit of type Vacation, Core counts a total of 8 + 16 = 24 hours against the hours used for vacation, as seen on the info bar for Vacation Time in Employees > Human Resources > Benefits.
This means your employees have to either enter time entries or add a benefit usage (not both) when making use of their accrued benefits. Core tracks these two independently of one another. Check the Core Help for more on Benefits and Benefit Usage.