I suspect Patchouli was the culprit. Just as she was casting some kind of spell Marisa broke in and the sudden noise caused Patchouli to lose concentration leading to the spell going haywire, uselessly draining all her magical power and knocking her out. Seeing Sakuya was just part of a dream she had while unconscious. And because Marisa was too busy looting the books she didn't notice Patchouli at all.