They could have contacted someone. Frontier gave them an oppurtunity to do so and it was easily within their power at Frontier to alter a flight plan - I'm sure they would have obliged but, as always, gave the player group a choice: link
How could Canonn have had no idea?
Because they didn't. It's clear that SOMETHING might happen when the jump took place, but because of the Galnet article coming out too early, we all knew what it was - and I can absolutely guarantee you that Canonn's council knew nothing about it.
Canonn are blameless for this - I mean, SOME of this thread wouldn't even exists if it wasn't for that Galnet news item... but even so, the whole this was clumsily executed. It COULD have been epic - if all the mechanics worked as they should.. BUT that isn't what happened.
It's not the story, nor the Thargoids people are upset about. It's the delivery.