And of course the pathogen's host parasite has eggs hatching out all the time also. Zapping doesn't kill eggs. Darn. So it could have come from that.
The sycrometer likely wouldn't miss detecting them, as much as indicating the frequency range was narrow enough to count as dead. Dr. Clark did discover that zapped creatures never recovered their full range of frequencies even if they lived, and that they usually died soon after, anyway. Maybe she didn't worry then, if they were completely dead yet?