Numbers too large in table of contents, etc.
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 techniques from that answer may be employed to make the numbers fit:
Memoir has another mechanism for the job:
section, or whatever; the
indent specifies the “margin” before the entry starts; and the
width is of the box into which the number is typeset (so needs
to be wide enough for the largest number, with the necessary spacing
to separate it from what comes after it in the line.