I have a few examples from the social development sector

1. Micro credit / Micro finance as means of poverty alleviation in most parts of South and East Asia : The grand ‘success’ of the Grameen Bank micro-credit programme spawned replication but research (http://www.devex.com/en/blogs/the-development-newswire/dfid-study-debunks-success-of-microfinance) now shows that it did some good but ultimately did not raise people from poverty. This could be seen as a programme failure but there were some unintended consequences. (a) governments and NGOs took micro-credit / micro-finance as the panacea for poverty alleviation and ended up over (and wrongly) using it without making a dent on poverty, (b) innovation around poverty alleviation dried up and policy makers refused to see reason and programmes beyond micro-credit, (c) spurious micro-finance / micro-credit agencies (businesses) sprang up all over the place leading to over-reach and people having multiple debts from different competing agencies, (d) increased competition for the space, led to underhand actions and corruption (definitely in South Asia). All of this while the fundamental causes of poverty were sidelined.
2. Banning use of DDT, intended to prevent harm to humans who consume DDT (used to prevent pest attack on stored paddy for instance) crippled the fight against malaria (http://www.acsh.org/healthissues/newsid.442/healthissue_detail.asp) leading directly to millions of avoidable deaths around the developing world while, perhaps, having limited impact on human health.
3. Food Aid and unconditional cash transfers over a long period of time in chronically food insecure areas in Africa have been known to deliver short term gains but resulting in long term dependence of the poor on aid. Local economies in large parts of Africa are known to be dependent on aid.
4. Continued use of Reservations for socially marginalised communities in academic institutions and employment in India has just led to more and more groups ‘demanding’ to be classified as oppressed. Interestingly the architect of the Indian constitution himself had recommended that this measure be used for a short time only. Sadly it has proven to be like catching the tail of a tiger. No political party has had the courage to let go.
5. Non Formal Schooling in South Asia which has been touted as a huge success. But what does it actually do? It lets the State off the hook when it comes to responsibility of delivering quality education. We end up with sub-standard teachers imparting useless ‘education’ to uninterested students. This ‘education’ barely keeps the kids off the ‘illiterate’ list and yet leaves them with no skills to compete and earn a livelihood.
6. Responding to drinking water / irrigation crisis by drilling bore-holes deeper and deeper (all over the developing world) – leads to draining of ground water reserves that cannot be recharged. This ‘availability’ of water also leads to human settlements where none should be.