Ok I found my answer, for anyone having the same problem take a look here:
This seems to be a bug with Matlab (I'm using R2010b).
The solution is to change the assignment so that the value you want to assign to the index in the large array is stored within the method temporarily. The updated method would look like this:
function log(this)
temp = this.some_value;
this.large_array(1,this.current_iteration) = temp;
end
I hope there's a patch or Matlab R2011a fixes this issue.