It is possible that in Settings > Time & Expenses > Personal Time Off, you have assigned the same activity item for Vacation time and Comp Time. Because of this, every time your employees enter time using that activity item, it logs against their comp time. The employees may not be allowed or assigned any comp time in the first place, that is why it is showing up as a negative value. You need to correct the activity item for Comp Time in Settings to fix this.
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