Hair transplant doctor performed 50% less grafts than promised. Is this common?

You should get half your money back if your doctor did half the surgery.  If you had the FUE, chances are you were not the best FUE candidate. What we call FOX Negative (FUE Negative).  You end up will many transections.   Most doctors do not tell you of this possibility.You can ask how many attempts were made and how many grafts were successfully harvested.  You may have 2000 holes on the back of your head and only have 800 good grafts.  Rest may be transected (dead grafts) that may never grow.You will not know unless you ask.

According to my experience, this is is really common among non specialised, inexperienced doctors or companies that offer false expectations and create unrealistic goals to the individuals. In some cases clients are misled by "large" number of grafts related to small cost, things that are not achieved in the end. Finally, the result is non desirable.

Harvest numbers are not always achieved.  In fact, a place that always gets the numbers would be suspect.  What is more important is that they did an honest count and refunded for work not done.  Most of the time,the limitations are beyond the clinic control and they can only try to do the most they can without risking healing and recovery and results.  

I rarely fall short o what I predict but I have done over 15,000 surgeries in the past 24 years so estimating both an art and science. The doctors should have a reason for not hitting the agreed upon target and you should be entitled to know that reason. If you are not satisfied, get a second opinion. 

If your donor area was too tight your doctor probable decided to take less hair to minimize chance of scarring,  but you can ask for the money for the difference.