I think i have found a bug in the game. I have destroyed everything in mission 11 where you need to bring a explosive train into some mountain. I've done everything up till the last objective but for some reason, the trains won't move. I think it is supposed to have the trains move the car into it.
Not sure what do to. I've been waiting 2 hrs for this stupid train to move and end the mission

I don't know where things may have gone wrong in your game. I finished that mission without any problems.
That bit about the train and the mountain:
1 - Bring a unit (any unit will do) close enough to the fuel canister (the yellow marker on the tracks) to 'tag' it,
2 - Destroy the 'Train Line Control Center' just north of the tanker (the other yellow marker). Just to be sure, i destroyed all the buildings there,
3 - Using a Pegasus, drag the fuel canister (moving north). As soon as you pass the point where the tracks split, leave the canister and pull the Pegasus back. If you've done evrything right, the canister should be in the left tracks after that splitting point, and the next train that comes along should push the canister.
At this point i followed the train in a Hurricane, but i was greated by some nasty flak and i ended up turning back. A couple of seconds later i saw a scene showing the train entering the base, big explosion, mission completed.

Yea, did that. Problem is as soon as that train center gets destroyed, all the trains stop moving... Maybe i am not fast enough in moving the car onto the tracks?

By 'car' i assume you mean the fuel canister that's already on the tracks, right ?
I sincerely don't recall that mission having any time requirements. I guess i could replay that one mission just to make sure. I'll do it and post back here.
Edit:
Ok, i just replayed that mission and i took my sweet time to drag the canister into position after destroying the train center and the trains just kept on moving.
So i don't know why they stopped for you. Maybe it really is a bug or perhaps you did something (destroyed something) that you weren't supposed to do.
Take a look at the attached pics. The train center is already destroyed and the trains are still moving about.
Maybe you should try replaying the mission from the start ?

Saw the pics and did exactly what you did. It work. I guess I took out the power to the trains or something.

Just a note: It is possible to complete the mission even if you blow up the trains/ stop them from running. If you destroy all the enemies around the base, you can drag the fuel tank all the way there with the Pegasus, though it will probably take 2 or 3 since it's hard to get the tank to go under the bridges while it's attached to the Pegasus, which will probably explode if you crash it too much.

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I know this is an old topic but If anyone plays this still and gets stuck on this mission, I think i have an answer.

I had the exact same problem. Ended up playing the mission though 3 times and always the same.
Maybe I was just too much slower then most people who didn't get the problem. I got it every time.

In the end I worked out what the problem was.

The two trains coming from and to the mountain get stuck together where the tracks are very close together.
I carefully used a small gun to destroy the cargo on one of the trains to free them up and they started moving again.

Careful not to destroy the actual train though, that will fail the mission. Just aim for the back cargo part of the train.

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Then another bug: I destroyed every enemy in the island. Then I put the canister in the main line, then destroyed the wagons (not the trains!). Followed the train that engaged the canister until it enter the mission gate.

Saw the cut scene where the mountain exploded, but then I was granted with a MISSION FAILED! WTF???

The way this mission is supposed to work is that you put the canister on the train line, and the train will push the canister into the mountain, boom.

However, with a canister in front of it, the two trains collide against each other at the Y intersection halfway on the map and get stuck. blow up the second train (careful that you don't destroy the canister or the train actually pushing it), then just use pegasus to pull the train and canister towards the mountain's entry point. With a bit of momentum, you can cause it to still go into the mountain and finish the mission.

The devs acknowledged it as an issue at the time, but never got around to fixing it.

The direction the trains are moving is critical. The fuel car needs to enter the heavily defended doors in the northeast end of the map. If you move a fuel car onto a track such that a train (or you) pushes it into the southwest doors, the mission fails.

Watch the trains for a bit to ensure you understand when and what direction they travel, then pull the fuel car from the short spur near the south end of the tracks, nearby the switch building you have to destroy, forward a short distance until it's off the spur and onto the main track. You'll see the mission status update. Then watch the train as it butts into the car and pushes it northward to the objective. Hopefully, you've cleared out ground turrets and units along the way first.

Sometimes the two trains get stuck trying to pass each other near the north-center of the line, and the trains never move again. If that happened, shoot and destroy the cargo car of the southbound train. That will free them both up.

Another solution is to tow the tank car with a Pegasus all the way to the stuck trains. A bit of pushing with the car may get them moving again.