Two separate shifts will appears for each employee, if you create ONE SHIFT and add another coworker in the shift from Advanced Options. In this case deleting one shift for any employee will cause the shift for the coworker to get deleted with it.
How to Avoid this situation?
1. Create a separate shift for each individual, instead of creating one shift and adding coworkers in the shift.
2. Or try removing the employee from the shift by clicking the shift and click 'Advanced options' then clicking the 'X' icon for the employee you want to remove from the shift.