The bombs don't get replaced that I know of. You aren't supposed to do the steps out of order. I don't know that there's anything you can do about it unless you can find a way to take the second bomb off the wall and re-place it (don't try to destroy it, that'll just make the problem worse).
#Maelstrom Expedition. Bomb not going off.
iron warren
Yeah tried removing the bomb, logging in and out, and destroying the bomb. No fixes. Just restarted the prospect and speed running it for someone.
mystic cobalt
Just don't do it out of order. You aren't supposed to know about the 2nd location until you've placed the first. If you want to have someone start heading that way while you wrap up doing the second to get it done faster, great, just don't have them place it until it's time.