* The code can't be run outside the original researcher's undocumented special snowflake system
* A fellow scientist who understands the domain can't understand what the code is doing and so is unable to verify that it isn't making any mistakes
* It'd be really nice if there were some sort of test cases that could verify that the code in question produced results in line with what the scope of the paper in question considers to be established science in that domain before it was applied to the experimental data - probably not always possible, but it'd be good to at least try
Yeah I know this doesn't touch the dozens of other reasons the whole institution is in trouble, and for those reasons usually nobody who has the skill and time to properly review the code actually reviews it carefully. For that matter, most scientists aren't very good at writing code that's easy to understand and will run everywhere. Just one more set of things that ought to go on the list of things that really should be changed.