I'm also partial to the theory that they have a problem with source control, and that merging code sometimes overwrites a previous fix.
I'd put that down to a lack of an overall plan or vision, as there's almost always no consideration of second/third order effects. So many changes lack any strategic vision of the broader game design.
Take the mineral price changes that occurred. FD's intent was clearly "Lets give trading a bit of a boost" by bumping a bunch of mineral prices. But nobody[1] foresaw the effect this would have on delivery/source missions, whose rewards are tied directly to cargo value, and therefore horribly imbalanced them resulting in a nerf a month or two later. Clearly, never considered.
On missions, we then had the time when factors such as station distance got included in missions... but nobody thought "What about Hutton Orbital, or those other long-range stations?" and thus, Rhea and other farming was born. Likewise "Robigo long range slave trading" was another unintended consequence of not having range limits on interstellar mission offers, and just identifying "nearest possible station".
Continuing with missions... notice how chain missions/in-space mission offers are all but gone now? Not suggesting this is the reason why, but something you might've noticed is that most of them were bugged in one way, shape or form, or lacked the "balance passes" that normal mission board missions had received over time. Again, that's because these were overlooked... fixes to missions were just for "mission board missions" not "all missions where they occur", again a lack of overall vision.
And so on and so forth.
There's nothing inherently "wrong" with any of these implementations, it's just that they were never planned, which means they almost always had dags that needed cleaning up after the fact.... which all ties back to a lack of planning and strategic vision.
... of course, more cynically, there
is a strategic vision, and it's driven by the shareholders who want the "next big content update" for profits++... to achieve that, all these issues can pretty much stay as they are and my rationales aren't relevant. People don't buy games for their bugfixes.
[1] By nobody I mean within FD. For myself and numerous others, this was the first thing we checked, thus, it got nerfed pretty quick.