Late to reply so you probably figured it out by now but if you have not..
First make sure in tasks that you have the correct task box checked that will give you the correct waypoint. Once at the right spot scroll down through your action menu until you have the command to deploy the satchel. Than you will have more options like 'Touch of Bombs 1' or you can drop your satchel with a 30 second timer.
If it doesn't work there is an ammo crate near where the Doctor was held, you can rearm and try again.