The fact is that the microbes did clean out oil in gulf of mexico, but in very small quantities.
Scientists initially believed that the micro-organisms will be able to remove and digest a large amount of oil, but this didn't happen. The main reasons are:-
Firstly, The spill was very large- it is the latest spill that has happened ever. So, when such a huge spill occurred, the micro-organisms were not readily available.
Micro-organisms only grow if food is present. Generally oceans have less oil content., so the amount of micro-organisms is less. This small amount was not able to remove oil as expected.
Secondly. , due to very large spill, a thick layer of oil was formed. Thick oil layer blocks sunlight and oxygen supply to water. So, most of micro-organisms that require oxygen or sunlight was killed.
Thirdly, the spill occured not on top of ocean, but inside, in deep ocean. So, some oil rised to surface and floated on water. But large amounts of heavier oil formed layers inside the ocean. Micro-organisms can break oil only if its in the surface. These trapped oils could not be cleared easily.