These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Using a continue invalidates your high scores. Contrast with the other two games in the series, where using a continue will let you save the score you achieved on your first credit even if you continue.
The last two stages, where a single hit can result in a Game Over, were not received well with players or even Ysuer's fellow developers.
Smug Snake: Apparently ZODIAC Libra has a "self-Righteous personality, and when it sights the awakened Ophiuchus, it opens fire without hesitation to prove its righteousness."
That One Attack: If you don't destroy ZODIAC Libra in its penultimate phase, it will release continuous streams of concentric purple circles, while alternating between homing lasers that make lowering your defenses to attack difficult, and missiles that can't be shielded away. If you still want the points (1 million instead of 4 million), good luck not timing it out.
That One Boss: The latter half of ZODIAC Virgo, and the Final Boss, Libra. What makes them stand out is that your ship, now ZODIAC Ophiuchus, has an unlimited-use shield...but has been reduced to a One-Hit-Point Wonder. You still only get one life, so even a single hit results in a Game Over. Of course, both bosses take advantage of this to toss out unblockable missile barrages at you.
They Changed It, Now It Sucks: While not a severe case, some fans believe the change of how the Phoenix's shield meter recharges in v1.01 and onward made the game easier. To elaborate, prior to the v1.01 update, the shield meter stops recharging while firing your weapon; v1.01 changed this so that it will recharge slowly while firing instead.