How is the sea? On rough seas, the waves block your periscope view for a while. If it's too long the target will "unlock".
Now, if the seas are calm and the waves do not block your view, and you're close enough, then there's definitely a bug. It may be temporary though, one that goes away by restarting the game, or the patrol.

Weather is usually a factor there. If you have high seas, then the auto targeting system will lose track. Try going to about 5 feet above scope depth.

As soon as I started next mission it worked fine, another problem solved, now all of a sudden I can't get anyone to man the deck gun, when I check and see where everyone is stationed no one is in the deck gun spots and I can't drag anyone in there. Sorry for all the questions but a newbe is a newbe.

Actually nothing "eliminates" the problem. It is an attempt by the devs to simulate conditions of poor visibility, where you can see the image through the 'scope but not well enough for your crew to make an automatic ID, for example. You probably can't use auto-targeting either. It is a function of the current visibility and goes away when you get close enough or when visibility improves. It does not matter that you can see the image in the 'scope display just fine. It is just a matter of the visibility versus your crew's programmed sighting range. As they say, It's not a bug, it's a feature!