Substitution is a concept that depends on the convention of scanning English poetry according to foot-based meters derived from Latin prosody. The word has proved helpful in explaining why what was called, say, iambic pentameter included numerous feet that were not iambic. An extreme example of "substitution" would be King Lear's outburst following Cordelia's death:

                                        /  *     /   *    /   *    /   *    /  *
                                    Never, never, never, never, never.

One could say that there are five consecutive trochaic substitutions.

Like most terms used in prosody, substitution is arbitrary, inexact, problematic, sometimes confusing--but often useful as a shorthand way of explaining variation of an expected rhythm.
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