It may seem wrong, but in practice it isn't. My experience with researcher-written code is that it does things in a roundabout, ugly, inefficient, duplicated-library-function but ultimately correct way.
The programs are not complicated. They are usually just some implementation of an equation or some other method for transforming input into output. Researchers don't have hundreds of hours to invest in learning the nuances of the const keyword in C++ or whatever, so they hack it. It works.
Checking extensional equality of programs is a task that is impossible to perform. If code is not well written, there ARE bugs lurking in the sourcefiles that just are unnoticed. Only computer scientists and mathematicians seem to understand this and try to prove correctness of their programs/results.
The programs are not complicated. They are usually just some implementation of an equation or some other method for transforming input into output. Researchers don't have hundreds of hours to invest in learning the nuances of the const keyword in C++ or whatever, so they hack it. It works.