For in-page comments, you could add an extra HTML block, and use permission overrides so that it is only visible to teachers.
For managing issues, you could step up from using a wiki to using proper issue tracking software (like http://tracker.moodle.org/). Saadly, Jira, which we use there, is not free. The most popular free alternatives are trac and bugzilla.
Teaching with Moodle
Paper Based Templates
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