I imagine the “last seen” times are shown mainly to indicate whether users are still active members of the site, and if they are likely to have seen recent replies. For these purposes, a few minutes’ error is harmless.
It wouldn’t surprise me to learn that Stack Overflow’s developers—like those of many large websites—have decided, as a performance optimization, to allow some information to be cached, and updated lazily, to avoid the cost of providing a globally-consistent, up-to-the-minute view to every user.
