It's not about bugs, it's about CAVE's last bosses since the original Dodonpachi have the ability to generate a shield when the player is invincible(at the start of a new life, after using a bomb, etc), such that the player have to defeat them fair and square, as overwhelming them with extra lives won't work.
In the older games, the 'shield' used different logics such that locking the player's invincibility timer doesn't make the bosses do the same. However in Daifukkatsu and Saidaioujou, the boss WILL be invincible when you are as well.
You're able to 'destroy' the boss only because the boss has to self destruct after a certain time, since this is an arcade game, it can't make one player stay in a stalemate forever, it needs the next player to throw in some coins.