What is your biggest pet peeve when using email filters to organize your Inbox?

Most email productivity applications allow the creation of "folders" (ex. Microsoft Outlook) and others allow the creation of "labels" (ex. Gmail). But in both cases, the application allows you to organize emails by using filters or rules to automatically store them in a particular folder or apply a specific label for easy retrieval at a later time. The key distinction, however, is that an email can belong to only one folder at a time i.e., a 1-1 relationship, whereas a variety of labels can be applied on a single email i.e., a 1-many relationship. I love using email filter rules just as much as anyone that's interested in taming their email Inbox. But I sometimes find myself not reading an important email either until it's very late or end up missing it entirely because the email skips the Inbox (where I spend most of my time) when a rule is triggered. And that drives me nuts. I hear you saying, "then why don't you edit the rule so that the email does not skip the inbox when it is triggered?". And to that I would respond, "then wouldn't that defeat the purpose and original intent of the rule? What's the point of creating a rule if all your emails end up in the Inbox view?". That, in essence, is my biggest pet peeve when using email filters to organize my Inbox.