Actually it happens not only on SCUBA mission but everytime when you get closer than 50 meters under the water near any enemy, no matter how deep under water you are enemy will spot you switch alarm ON and will try to shoot you, sometimes they also uses even granades hah!
I understand that they can easy spot you when you swin on the top, but when you are diving 20 meters underwater its kinda impossible to be spoted, well for a player, seems like AI dont care about that.