Ship at the end of the AT-AT base attach sequence doesnt blow up.

Did you use the canons vs. just the lasers? If you just use the lasers you cannot destroy the spaceship. I believe it's left trigger. I had this issue and noticed after restarting the sequence a quick pop up message that canons are LT (or whatever control scheme you are using depending on platform).

If you are using the canons and still cannot proceed then it is a bug.