Yeah, the XF Ignore function is really pretty basic. It hides their posts from the Latest Posts widget but threads they post in still show up in What's New (only threads they start are hidden), which is probably why the alert still gets generated. Basically, the Ignore works on anything that is post-based, not thread-based. So, threads they start are hidden because they made the opening post, but threads they post in are not affected save that their posts are hidden.