Okay while looking for a way to get the bureau alerts to spawn for me, I found this post on reddit about it. That was pretty much the only answer I've been able to find on it so I thought I'd make a comment on here with some more detailed instructions in case anyone else runs into this bug and can't get the bureau alerts to pop up:
1) Copy your all of your Control saves to a USB drive.
2) Pick Chapter 3: Old Boys Club in the mission select menu (since Control doesn't allow for multiple save files, selecting a mission will overwrite your save but if you have it on a flash drive or in the cloud you can get it back easily)
3) A bureau alert spawns right away when you load in, so set up your guns/mods then fast travel to the control point next to the alert
4) Run forward until the enemies spawn then use launch as much as possible to clear out the enemies
5) The 3 targets that you have to kill to complete the alert will follow you back down the hallway one at a time where the control point is but you can cheese them there by going at the very end of the hallway and popping in and out behind cover to attack them.
6) Once you've killed all 3 targets, the alert is completed. Back out to the main menu, rinse and repeat 5 times to get the trophy.
7) Copy your USB drive saves back to your hard drive and overwrite the mission select saves.
Honestly this is probably a quicker method for anyone even if the alerts are showing up in your game, because there's no waiting around involved when you do it this way. Took maybe 30 min tops.
1) Copy your all of your Control saves to a USB drive.
2) Pick Chapter 3: Old Boys Club in the mission select menu (since Control doesn't allow for multiple save files, selecting a mission will overwrite your save but if you have it on a flash drive or in the cloud you can get it back easily)
3) A bureau alert spawns right away when you load in, so set up your guns/mods then fast travel to the control point next to the alert
4) Run forward until the enemies spawn then use launch as much as possible to clear out the enemies
5) The 3 targets that you have to kill to complete the alert will follow you back down the hallway one at a time where the control point is but you can cheese them there by going at the very end of the hallway and popping in and out behind cover to attack them.
6) Once you've killed all 3 targets, the alert is completed. Back out to the main menu, rinse and repeat 5 times to get the trophy.
7) Copy your USB drive saves back to your hard drive and overwrite the mission select saves.
Honestly this is probably a quicker method for anyone even if the alerts are showing up in your game, because there's no waiting around involved when you do it this way. Took maybe 30 min tops.