Duplicate Component Deisgnator
You probably have two components that have the same value in two different sheets, Example:

Sheet2 has   
J2  
J3  

Sheet5 has  
J2  
J3  


You need to rename the connectors in sheet 5 (or whichever sheet is offending)

Sheet2 has    
J2    
J3    

Sheet5 needs to be   
J4  
J5  


Manually check all of the sub sheets and see if any two designators are the same

If that doesn't work then designate sheet1 and sheet2 first with lower numbered designators (ie J1-J4) and sheet5 to have higher numbered designators (ie J4-J5) so when it repeats it fills in J4-J20