LaTeX constructs the table of contents, list of figures, tables,
and similar tables, on the basis of a layout specified in the class.
As a result, they do not react to the sizes of things in them,
as they would if a tabular environment (or something
similar) was used.
This arrangement can provoke problems, most commonly with deep section nesting or very large page numbers: the numbers in question just don't fit in the space allowed for them in the class.
A separate answer discusses re-designing the tables and those techniques can be employed to make the numbers fit.
This question on the Web: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=tocloftwrong