Uganda (or at least northern Uganda) has been pretty stable for a while, Kony has been out of that region now but this only gets a brief mention in the video. The group supports working with the national army in Uganda who have been accused of doing actions similar to what Kony does. And of course IC hasn't even brought up the question of why
Kony was able to get away with this shit for years in the country or the government's involvement with this issue.
You can read the most popular critique here
and check out what some Africans involved in a similar effort are saying about IC here
There's nothing wrong with good intentions and rallying massive support to stop a war criminal sounds great but IC are shining a really dim, ignorant and somewhat offensive light on this issue to paint it in black and white so they can twist it into a more accessible narrative for the public.
And some other fun items: The movie screened in Uganda but was stopped midway after people started throwing rocks in anger
and Jason Russell, the guy who spent a chunk of the Kony video blathering on about his wonderful life and white child, just got detained for masturbating in public