One issue is that internal science within a company/lab can move incredibly fast -- assays, protocols, datasets and algorithms change often. People tend to lose track of what data, what parameters, and what code they used to arrive at a particular figure or conclusion. Inevitably, some of those end up being published.
Journals requiring data and code for publication helps, but it's usually just one step at the end of a LONG research process. And as far as I'm aware, no one actually verifies that the code you submitted produces the figures in your paper.
It's a big reason why we started https://GoFigr.io. I think making reproducibility both real-time and automatic is key to make this situation better.