I think you need the marine in there to drive it.

I know - I wrote the diver, and that's the marine. It still doesn't move.

Look below for the ending of that mission walkthrough to see if you're missing anything. The full walkthrough is here.
***** WARNING - SPOILERS BELOW *****
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Finishing up the Mission:
You should have killed all enemy soldiers except for the patrol group. Make sure that your Green Beret has opened the northern floodgates, and your Sapper has placed a remote bomb near the fuel tanks. Have everyone rendezvous in front of the tank garage. When the patrolling guards are far north, have the Driver move the truck in that area in front of the tank garage, blocking the entrance. Get everyone in the boat, and take the whole crew down to the area where you began the mission. Your Marine can then scuba toward the sub and enter it.
Once he's aboard, get the sub in position, fire the torpedo at the bow of the ship, and once the torpedo is launched, do a quick turn around and head for your crew at the south end of the map. Your Sapper can also exit onto the shore and detonate the bomb at the fuel tanks. Don't be in too big of a hurry to get out of the sub, as a boat shows up near the escape buoy, ready to cut your life raft to shreds. Luckily, the sub has two torpedoes, and can easily take this boat out of commission. Dock the sub near the southwest, have the Marine scuba back to the raft, and row everyone to the escape point.

Yes, but the problem was that the sub wont move forward. I can move it backwards, parallel with the dock, but it won't move forward or to the sides.
I'll restart the mission and see if it happens once more.

That's a good idea. That way you can make sure you didn't hit a weird bug the first time around .

I did have this exact same problem, and it occurred for me before I had set off any alarms. I was eventually able to get past it just kind of through dumb trial and error stuff. I found the sub could slide backwards, and if I did it *just* perfectly, it would achieve a very small amount of separation from the dock, and that if I then commanded it to move forward *just* perfectly, I could get it out past the dock where it could maneuver. Any wrong step and it would get hung up though, it was extremely frustrating and probably took me 15+ reloads to get it to work right.
Actually, this is my biggest complaint with what otherwise I think is an awesome game, I pretty regularly have 'getting hung up on scenery' problems when trying to drive vehicles of any type.

How does the sub fires a torpedo ????

I had exact problem and I've never set the alarm. So, the solution is what user 'gwin' suggest: it's just a bug, but you can easy manage it.

When you jump in this boat, remember to don't click anywhere. You need to do "one click" (only one!) perfectly in a straight line of that boat to move it. Wait, and when boat will leave place, you can move it just like other vehicles.

Lunch torpedo with standard "CTRL" + point.

That's all. Thank you, officer. :)

Thanks gdwin! Clicking this exact spot as the first click after boarding the sub seems to work for me. Take a look at the image.

Hey guys!

I've got the bug too, the solution is:

Click SOUTH from the minisubmarine. Any southern point below it could help, beyond the dock.

One click is enough, the submarine will react immediately.

Hey, thank you very much!!

Thanks. Worked for me.

That small tip did the trick!!