The issue with Harvester AI is that they are programmed to avoid threats, but the programming is really buggy, and only causes issues, and doesn't actually work properly as intended.
The issue with fixing Harvester AI is that it makes it too easy to control harvesters and makes it too easy to defend infantry rushes and some-what changes the game meta.
As Black mentioned, previous versions of Vet. patch 'fixed' the faulty AI, but a few players were complaining that it made infantry rushes a bit overpowered and they had a point.
In current version of Vet. patch, the Harvester AI does listen a little bit better than default, but it is not nearly as smooth as in previous versions.
A lot of these issues should have been patched by WW, but they got bought out by EA and were forced to work on other projects. This is why they never fixed Harvester AI, finished adding veteran upgrades to units, fixed glitches like tanks/artillery not being able to deploy on tiberium or terrace edges (even though there is an option for it that doesn't work), originally harpy / orca fighters were orignally supposed to be able to shoot other aircraft down, but they didn't finish coding it. 2.03 was the last update they released, that mainly nerfed NOD, in which they would have observed the changes, saw they over-nerfed things like cybrogs (making them absolutely worthelss), and continued to balance them out. Many other examples, and if anyone talks to the original developers they will agree with all of this and more.
The problem is that people got used to playing a broken game and some players are stubborn and like it that way, but regardless the concerns with harvesters being too easy to control nerfing inf rushes was valid IMO.
As far as Carryall AI, that is hard coded, Xme has already released a few patches that fix issues, but no one has been able to consistently replicate certain glitches to the point where he was able to narrow down the code causing them (for example two disruptors landing and sticking next to each other with the carryall not releasing).