At my school if we do any extension course i.e. English Ex. 1 or Maths Ext. 1 we have to do another one unit course, as a 13 unit pathway will not be run. Is this the same for anyone else?
That doesn't sound right. Plenty of people take only a single one-unit extension course. I thought that was standard across the state. I think you should consult your school further, if not the Board of Studies about this.
We can do only one extension course but we have to take another 1 unit course so it is 12 units. However, if we only do a 13 unit pathway the extra unit is offline.
No that's completely wrong you should be allowed to do however many units you want as long as you meet the requirement of 12 units minimum in year 11 and 10 units minimum in year 12. My friend did 14 units in year 11 and I did 13 so you should not be facing that problem, this is even stated on the nesa page: http://educationstandards.nsw.edu.au/wps/portal/nesa/11-12/hsc/subject-selection
If they don't let you only take 3 unit without taking another extension then you should take it up with nesa