Mermin-Wagner theorem tells you that if there is a long-range-order (existence of BEC) in two-dimensional systems, the fluctuations will drive the system to somewhere else, destroying the condensate. Yes, as puzzly said, it is the long-wavelength phonon that destroys the coherence of the infinite system.
Another way to view it is that the atoms have fewer freedom to move in two-dimensional space than three-dimensional space. The effectively stronger interaction between atoms make the long-range correlation impossible.
For Kosterlitz-Thouless transition, it is about the existence of another phase at low-temperature with quasi-long-range order, despite the absence of true long-range-order. In 2D Bose gas, it is the superfluid phase.
But since bosonic systems are all prepared in a trap, the finite-size effects play a big role. I suggest reading the experimental report PRL 102, 170401 (2009)