We can't diagnose what we cannot see...
At least attach a sample file and the code -- but, if it is something that is provably intermittent in producing different results from the same file with the same code at different times, then it's not likely anybody here can help.
That would be either an inadvertent "operator error" like renaming a MATLAB builtin with a user-defined function or the like (that is certainly easy enough to do) or some other OS or competing application that is causing a machine failure. The latter is probably the least likely cause...
But,it would take a real case of the occurrence to be able to have any hope of uncovering what is happening unless it were an overlooked issue in the script that is either data dependent or there's a second operation that introduces the fault that occurs only part of the time.
