Anti-Climax Boss: Demon Apsu with Sailor Chibi Moon's party. She's really strong when fighting Sailor Moon, but when fighting Chibi Moon she gets much weaker.
However, there ARE two endings to this game, and you need to kill Demon Apsu when she's at full strength to get the "good" ending (and THAT battle proves to be much harder), so such trope makes a lot of sense given the much lower reward.
Demonic Spiders: The U-tahime enemies at the North Pole in chapter 4, due to spamming their Fascination spell.
Fan Fic: There was actually an RPG Maker XP game based off Sailor Moon Another Story aptly named Sailor Moon Another Story 2, it takes place AFTER Sailor Stars which more a less does the same thing with a similar story but does call backs to Sailor Moon Another Story, the anime, and the manga all at once. It does take more liberties and has Sailor Galaxia as a re-chaos possessed villain, of course Queen Beryl (she gets resurrected ALOT in everything from Sera Myu to Fan Fiction, to even video games) it also features mixes of manga and anime attacks, has the Sailor Star Lights show up, and even Sailor Cosmos eventually. As with the original it is a Continuity Snarl.
Game Breaker: Time Stop. Sailor Pluto can use it battle after battle (or with MP-recovery items, several times a battle) and the enemy can do absolutely nothing about it.
Sailor Saturn, who if equipped correctly, can steamroll enemies with her Death Reborn Revolution attack, which also has a tiny cost of MP.
Uranus and Neptune's combo attack can be led off by Uranus, who (barring Saturn) has the strongest offensive stat in the game, and do ridiculous amounts of damage, while her negligible defense can be covered by Time Stop. An Outer Senshi party is layered with Game Breaker upon Game Breaker.
Another pretty bad example has to do with Link Up moves in general, in that the same move can be used twice per turn, with the only penalty being MP usage. For example: If it is Moon's turn and you use a Link Up move with Uranus, Uranus can select the same Link Up move with Moon and pull off the move twice that round.
The Defend command in general. Drops virtually all damage to single digits and increases your evasion by quite a large amount. It's perfectly possible to just defend until the enemy runs out of MP, meaning you only then have to worry about a physical attack targeting the one person doing your attacking, or a Confusion-type spell slipping past.
Poor Sailor Saturn had to watch her father Doctor Tomoe die in front of her eyes. Ironically, if you chose the better option of fighting Stone Dagger, the Daimon that took over Tomoe, you get much sadder music playing as Tomoe dies.