The simple answer is that certain stretches of a genome contain sequence that is difficult to sequence, mainly due to repetitive regions, tracks of the same base, GC composition, closed DNA, etc. Searching Google for "gaps genome" brings up a whole host of references about the causes of gaps and the attempts to close them.
Note: even within the euchromatic regions there can be long runs of Ns representing gaps that we can't fill yet. In many cases we do have a good size estimate for the gap- typically based on experimental evidence like comparison to an optical map. For human, the problem is that some of the euchromatic gaps are polymorphic, so the size of the gap really depends on the individual you are assessing.