You have highlighted two totally different aspects of aid and charity - I have little doubt that much of the aid to developing countries provided by the West via NGOs is lost through waste and corruption.  How big a problem though is by its very nature is difficult to assess.  In the example quoted in your first link it claims that $7 million had been misappropriated from the total grant of $474 million made by the Global Fund to Fight HIV/AIDS - certainly a lot of money yet still less than 2% - I'd be very surprised if the overall figure for all national aid were as low as this!

The second problem you highlight is the amount of the funds raised by charities that actually ends up being spent on those the charity is set up to help.

The article you linked to unfairly criticises Oxfam in my opinion.  They have lumped together all the income the charity receives and compared that to the amount that is finally used to achieve its aims.  This is totally unreasonable.

If we take an imaginary charity that has a number of income sources.  Let's say they receive £1,000 from donations and their collection, advertising and admin costs were £100 then that would mean 90% was spent on their aims, good by any standard.  Now suppose they decided to sell goods to raise funds, maybe T-shirts, calendars and cards.  They sell £1,000 in goods but production and other costs account for £900 leaving £100 to add to the previous £900 available for the aims of the charity.  The causes sponsored by the charity benefit by these activities but the overall figures for the charity look decidedly less attractive - £2,000 raised, £1,000 in costs leaving just £1,000 to be spent or 50% of the total raised. 

That is the way the article has treated Oxfam's income.