To understand how you end up with a length of 11 for your usedsubsets you must consider not only the traversal order(1)(2)(3) in which the expression is scanned for pattern matching but the evaluation order as well. Much like Map as I summarized in Scan vs. Map vs. Apply Replace does not perform a sequential evaluation* but performs all replacements and then evaluates the entire expression.
If we change the head of your expr to Hold we not only witness the behavior described above but also clear illustration of the source of 11:
expr = Hold[1, {2, {4, {5, 6}, {7, 8}}}];
usedsubsets = {};
Replace[expr, x : {__} :> (AppendTo[usedsubsets, x]; Sequence @@ x), Infinity]
Hold[1, AppendTo[
usedsubsets, {2,
AppendTo[usedsubsets, {4, AppendTo[usedsubsets, {5, 6}]; Sequence @@ {5, 6},
AppendTo[usedsubsets, {7, 8}]; Sequence @@ {7, 8}}];
Sequence @@ {4, AppendTo[usedsubsets, {5, 6}]; Sequence @@ {5, 6},
AppendTo[usedsubsets, {7, 8}]; Sequence @@ {7, 8}}}];
Sequence @@ {2,
AppendTo[usedsubsets, {4, AppendTo[usedsubsets, {5, 6}]; Sequence @@ {5, 6},
AppendTo[usedsubsets, {7, 8}]; Sequence @@ {7, 8}}];
Sequence @@ {4, AppendTo[usedsubsets, {5, 6}]; Sequence @@ {5, 6},
AppendTo[usedsubsets, {7, 8}]; Sequence @@ {7, 8}}}]
Lest you think this has anything to do with AppendTo, Sequence, or even CompoundExpression or Hold, here is another more generic example:
Replace[List @@ expr, x : {__} :> f[g[x], h[x]], Infinity]
{1, f[g[{2,
f[g[{4, f[g[{5, 6}], h[{5, 6}]], f[g[{7, 8}], h[{7, 8}]]}],
h[{4, f[g[{5, 6}], h[{5, 6}]], f[g[{7, 8}], h[{7, 8}]]}]]}],
h[{2, f[g[{4, f[g[{5, 6}], h[{5, 6}]], f[g[{7, 8}], h[{7, 8}]]}],
h[{4, f[g[{5, 6}], h[{5, 6}]], f[g[{7, 8}], h[{7, 8}]]}]]}]]}
This is merely the result of the "inside-out" replacement you referenced in your question.
*The exception to this statement is the use of either RuleCondition or its more verbose cousin, the Trott-Strzebonski in-place evaluation technique. These cause early evaluation of the RHS of the rules, after pattern substitution but before replacement in the main expression.
Replacedoes a depth-first postorder traversal of the expression tree. See this very interesting thread for a discussion of the topic. – sebhofer Dec 03 '14 at 10:46