Okay! Thanks for the great responses everyone. But there are still unanswered questions. Who died in the Agrius? If it was the warship the Empire make it out to be, it sounds like it would have required a lot more guards/personnel. If the Agrius was as stocked with people as it should have been, where did the Empire get the numbers to restock a huge part of a legion? If it was from subjugated cities, why would the Garleans leave enough people to restock an entire legion. That's easily enough people to rebel against Garlean rule?

This part is less lore like and more technical, but the castrums don't make any sense. At the moment there are 4 visitable castrums, each with their own cohort. It goes:

Castrum Meridianum- 8th Cohort
Castrum Centri- 5th Cohort
Castrum Marinum- 4th Cohort
Castrum Occidens- 2nd Cohort

We know there are at least 5 castrums that are Garlean occupied, with an abandoned one in Coerthas. Wouldn't it make more sense for it to go:
Castrum Centri- 5th Cohort
Castrum Marinum- 4th Cohort
Castrum Oriens- 3rd Cohort
Castrum Occidens- 2nd Cohort
Castrum Meridianum- 1st Cohort
Why are there 8 cohorts in a five castrum system?