That's the whole trouble I've been having. For some reason, on my end many of the hardpoints such as the torpedo tubes and phasers are centered toward the middle of the ship. So in the MPE, they look like they're in the center, but in game they look like they're firing from the normal positions i.e., aft phaser from aft strip.
Please take a look at the photo I included. It looks like the tube direction is coming from just above the center impulse engine.
Because they were centered, I had to move it 259 units back so it'd be in the canon location. If you also notice, I deleted forward tubes 2-4 and aft tubes 2-4. I make the Galaxy have only 1 tube fore and aft as I did in KM so it's like the real deal.
In summary, some weapon hardpoints like the torpedo tubes are at center of the ship and when I moved the torpedo tube to canon location it wouldn't fire.
****UPDATE****
I also used the pick tool to click on and select the exact location of the torpedo tube on the ship model in MPE, then used get in the properties to apply the location.
I have also noticed the scale in MPE was set to 1. I have now set it to 0.01 and the orientation of the property now lines up correctly on the model in MPE. I hope this will help but I do not know if I will still have the issue with the torpedo being unable to fire yet.