Lakes generate within other lakes and oceans...and water bodies in general. I have seen this in much older version as well but it was always been a rare bug...until now at least.

On the screenshots:
2013-07-07_23.32.48 the biome is FROZEN RIVER.
~23.33.03 is also FROZEN RIVER
~23.33.55 is a lake in a Taiga

I have also seen some in the Ocean biome. Sometimes it is in the form of a cube or parallelepiped оr a cube underwater. Sometimes it is just a "lake" in the ocean.

The new way in which water manages itself clears out the "ocean lakes" but not the air parallelepipeds.