There are quite a few reasons why a BP timer would be wasted, sleep, stun, terror, a mob dying after use but before it goes off, your pet dying before it goes off, etc. I'm sure people could list more.
Perhaps treat it in the same way as a paralyzed spell if it does not go off? Maybe give SMN a new job trait that shortens BP recast if it does not activate? I don't know, those are just suggestions. This has bugged me for a long time.
Even with the bp timer reduction gear that exists now, I still think it's unfair when it happens, especially considering how important BP's are to the job.