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I'm a newer player and i've always taken the trygon prime upgrade as a double wammy to deep strike in with my doom. Tonight when i was thumbing through the codex i noticed as usual the containment spines says trygon prime only, which is fine. But the standard attack that comes with the non prime (bio-electric pulse) doesnt have anything stating that a prime can't also use that attack. As per monstrous creature they can fire two shooting weapons a phase. So have i been missing out on firing my bio electric pulse on top of the containment spines? If so, dang, thats a free 6 shots i'm throwing away.

From the trygon page (pg.50): "A Trygon Prime uses the following profile when firing its bio-electric pulse [Containment spines stats]"
So yes, you've been playing correctly.

Yeah, containment spines is just an upgrade to the bio-electric pulse. Not a separate gun.