Theft or misappropriation of aid money in Afghanistan is a big issue. But it's an old problem, that's become worse in the last half century, as colonialism disappeared, and much more cash became available for foreign aid development projects. One problem is that the foreign cash often comes with strings attached, even when the donors don't realize it. For example, most of the aid money comes from Western democracies. The donors believe democracy, women's rights, and a whole bunch of other Western practices, are good things. But the recipients, or their local leaders, often disagree. Thus the aid money becomes less welcome, and tainted. Thus diminished, it's easier for the locals to justify diverting the aid money to other uses. The local leaders will often keep a lot of it for themselves, but more often, the money will be spread around, and the guy dispersing the cash will be more appreciated, and powerful. That's important because at the local level, in most poor nations, there is a form of democracy. Leaders are selected, if not by a vote, than by consensus. These leaders are usually rich or powerful, and seen as better able to take care of his neighbors.
Local politics also influences how aid money will be used, or misused. Villages often have jealous neighbors, something made worse if the neighbors are from a different tribe or ethnic group. This will sometimes cause aid money to be misused to buy weapons, or even hire mercenaries, to aid in taking something from the neighbors. Within a village, there are often two or more factions constantly competing for top leadership jobs. Thus a large chunk of foreign aid money has the effect of throwing kerosene onto a fire.
The biggest problems are often culture clashes. The foreigners coming in to administer the aid projects, and cash, often had very different ideas about how life should be lived. There was usually agreement, with the locals, on the need for better medical care (including sanitation) and education. But even here there can be problems. In many cultures, it's considered bad manners (or worse) for male medical personnel to treat females. For schools, there are often disputes about what should be taught. Reading, writing and arithmetic tend to be non-controversial. But not always. In Islamic countries, religious studies are often considered more important than any other kind of learning. That might include learning Arabic (the language of Islamic scriptures), which is preferred to studying the local language. Educational issues usually divide locals in Islamic nations, with many parents more concerned with economic success for their kids, and that means studying anything but Arabic. Since Islamic conservatives, especially the clergy, sometimes get violent when they encounter opposition to religious studies, people often die over such disagreements. The aid donors get caught in the middle, especially now that such a disproportionate number of Islamic terrorists come from Islamic religious schools.
Then there are generational differences. The elders in a village tend to be more conservative, while the young people (from teens to 30s) are more agreeable to change. This creates divides, which have become more widespread with the arrival of cell phones and the Internet. In the last decade, the tribal territories of Pakistan have seen a sharp increase in these generational conflicts, with many of the younger men using the Taliban as a vehicle, not to institute a religious dictatorship, but to make it easier for them to overthrow the traditional tribal leadership, with new ideas of all sorts.