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These are two different kinds of universes. The one that Rose is in is called a "parallel" or "alternate" universe, and was said to be of the kind of universes that branch off from another universe whenever a decision is made or an action is taken, forming an alternative universe in which a different action or decision took place and thus set history on a different course ("Doomsday"). These universes are separated from each other by the "walls of reality," which were sealed after the Time Lords were put in a time lock. Because the walls of reality are closed, the Doctor cannot cross over into these kinds of parallel universes.

The universe in "the Doctor's Wife" was described as a "bubble universe," or another pocket of space that is connected to the universe by a time rift (like a small soap bubble forming on the skin of a larger soap bubble, hence the term "bubble universe"). The Doctor is able to enter bubble universes because they are connected to the primary universe by a time rift, which can be easily traversed - there are no "walls of reality" dividing the universe from any smaller "bubble universes."