Why are Emails trapped by a filter and marked as junk alerted?

Having to deal with a lot of junk mail in the last days I’m now heavily using Thunderbird’s filters. This works great, but I don’t understand, why Thunderbird alerts even Emails that are marked as junk and/or failed to pass my filters. This is can be very annoying. Wouldn’t it make sense to have alerts triggered only by those Emails not being marked as junk or even better, not being shifted to junk, spam or trash?
TB should at least offer an option to enable such a behavior, e.g. when customizing a filter.