I haven't tested the it extensively, but I have heard that when senders change the email subject -- especially when they remove then tracking token -- that the tracking will often fail. This is expected. CRM uses a combination of the sender/recipient/subject/token to determine whether email messages are related to each other. So if the subject changes then the determination is made very difficult.
The good news is that people replying to email messages do not often change the subject. But unfortunately there is nothing you can do to prevent them doing so.