First of all, the guy who made that film get's paid $90,000 a year. That's for him and his family. This does not include him paying costs for film equipment, video editting software, nor does it cover travel or accomodations whilst in anywhere else. Those are all covered under the ludicrous budgets that the Invisible Children organization actually deal with. Let's go to that now. Here are some expenses from CharityNavigator.:
Compensation of Leaders | % of Compensation relative to amount of money made by IC | Title
$88,241 | 0.99% | Ben Keesey - CEO
$89,669 | 1.00% | Jason Russell - Co-Founder/Filmmaker
$84,377 | 0.94% | Laren Poole - Co-Founder/Filmmaker
Revenue
Total Contributions: $10,334,060
Program Service Revenue: $3,423,351
Total Primary Revenue: $13,757,411
Other Revenue $7,769
TOTAL REVENUE: $13,765,180
Expenses
Program Expenses: $7,163,384
Administrative Expenses: $1,444,570
Fundraising Expenses: $286,678
TOTAL FUNCTIONAL EXPENSES: $8,894,632
Payments to Affiliates $0 Excess (Or deficit) for the year: $4,870,548
Net Assets $6,584,811
As if that isn't bad enough, they've refused to Co-operate with the Better Business Bureau, Their transparancy rating is fairly low on Charity Navigator, and allegations of fraud. HuffingtonPost has an article on it here.
Besides, they make a fairly large point about sending money to the Ugandan Military. This is a big no no for a couple of reasons. First of all, Kony isn't even in Uganda. Funding a military that has no real authority over another country to LOOK in other countries, is a moronic idea to begin with. Secondly, the Ugandan military is already using this as an excuse to enter other countries and exploit resources from surrouding areas. The Government of Uganda is full of criminals that are worse than Kony himself. Not to mention the bloody PRESIDENT of Uganda is responsible for millions of deaths. Then you've got allegations coming out that Kony is already dead. The LRA (Konys ragtag bunch of assholes) isn't that large, or all that active.
The worst thing about Invisible Children (In my opinion) is that they lobbies for DIRECT MILITARY INTERVENTION IN AFRICA. After all of the terrorist hunts in the Middle East, and having troops stuck in Afghanistan and Iraq, don't you think that the people would have learned by now that having troops in another country to hunt one asshole isn't exactly the best idea? Especially when some of the Republicans believe that invading Iran is a fairly good idea at the moment. There are SERIOUS issues with this group, issues that people are overlooking. I will admit that at first I was already on Twitter and ready to bitch at people about the injustice that's being served in other countries and then I decided to look into the organization. The information is there, and willing, but people are fearful to even look. Fearful, lazy, or just swept up by the movement. Injustice exists in the world. It is damn stupid, and it sucks ass, but that's the nature of this planet at the moment. Humanity, since rising from the primordial ooze, has killed people over far less than anything you could imagine. Then there's the fact that if Kony is alive, and the ICC, or International Criminals Court, manages to put him on trial, what's it going to achieve? Numerous war criminals have stood trial before the ICC. This isn't a game of chess. You don't topple a pawn and move on. The pawns replicate. It's like fighting a hydra. If you slice off one head, more are going to pop up in it's place. You remove one player, and 10 others will appear. Hell, there's a case to be made that awareness driven ngos perpetuate the current state of afafairs and are an intergral part of the current system of global unfairness. They ovver placebos for guilty consciences and as such, they don't change anything. If you think of large entites such as Global Corporations, conglomorates and powerful nation states that capitalize on injustice, corruption and disorganization and exploit the poor for their resources and manpower, the best thing that could happen to them are programs such as this. There's a lot of reasons why Invisible Children has a good idea of what they're doing, but FAR too much on the opposite sides of the scales to tip myself (and no doubt others) into not bothering with this group and it's practices.
Information retrieved by use of google, and a variety of different comments spread across Kony2012 post comment fields.

All credits go to Lord_Cade of the reddit community.