The logic in your 'if' part is faulty. When you do the test "find(newArray(i))==d", you are doing a test on a single-element vector and the answer would always be 1. Testing whether d==1 is meaningless, and in any case in your subsequent replacement if the 'if' turns out to be true there is no guarantee that you will not later place the same 'd' in another position in 'newArray'.
To make your basic strategy work properly, you need to pick out elements one-at-a-time, as you are doing, and place them in random positions in newArray but keep reducing the available locations in newArray so that no other value gets placed there. In other words, you need an array which keeps shrinking in size, of all the available locations in newArray. You can make use of the [] operation for this. That way you can avoid overwriting previous entries into 'new'Array'.
It pains me to see the problem done in this way, however. It is much more efficient to do as Mathworks has done, to provide n random numbers from 'rand' and sort them using 'sort'. The associated permutation would give you the desired result. However, if this is homework, your teacher might object to this.
