Oh damn! Thanks so much for reporting. Didn’t think of that. I take it you touched the ship while their shield was down? The shield should protect from the bomb but didn’t remember touching triggers the bomb too.
Actually I found that if you go right up to the ship while its down the small radius plus beam shortens the fight so in my brain I thought maybe when the shield is up the small radius might go through the shield (don't ask me why I thought that) anyway it doesn't and I got nailed by a ball which activated the core and blew up the boss ship