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.
Anti-Climax Boss: The Chaos Lord built up to be the evil prince of Digimon that the humans were forced to flee to another continent from. Yeah he's just a Machinedramon Palette Swap who spends most of the fight guarding or using weak moves. Doesn't help that he's fighting alone in a game where 3 on 3 battles are standard. Neo-Crimson isn't much better.
Game Breaker: Attacks that cause Confusion. Confused Digimon attack themselves or their allies. If you confuse all 3 of your opponents, you win. The only way to fix Confusion (Well, players can use items, but the computer can't) is with the Friendly Fire attack, which the computer is rarely seen using.
This would be the case if confusion didn't wear off whenever it wanted too. And it will usually wear off for the computer before it would a player, sometimes on the same turn it was confused.
You can also avoid damaging yourself or your team if you instruct the confused Digimon to use an 'interrupt' attack. It will attack the same way a non-confused Digimon will.
The attack Duo Scissor Claw is the real game breaker here. It lowers the defense and damages an entire enemy team at the same time.
Add to this any move that lowers enemy stats alongside damaging them. When this game hits something with debuffs, it debuffs them hard.
Among others, recruiting certain Digimon. It requires you to fire gifts at them in the field. Then battle and defeat them, but the gifts are separated by the three types. Only the team the player chose will have gifts available for that type. It isn't until the device dome that the player can reliably get Digimon of the other two types and even then you're restricted to low-level gifts for a large part of the game.
Also, due to the aforementioned variation in enemy Digimon movement, depending on the kind of Digimon you want, it can be really hard to be able to fire enough gifts to get them to join you, as they move towards you too fast. Unless you happen to catch them stuck behind a trap, but that's very luck-based.
That One Boss: Crimson. When you fight him as the Disc One Final Boss, he is by far the most powerful fight in the game. Unlike Damien who (being the first person to use a Mega against you) brought a rather pathetic Puppetmon, Crimson brings a Skull Mammothmon, which has a very powerful all attack for that point in the game. It's a shame that the next time you fight Crimson, he's actually weaker.