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.
Jua-Mu Dalby is pretty monstrous. At first, he was just a normal fanboy of Al-Van Lunks, but once Al-Van got demoted, he takes a swing in Ax-Crazy and becomes even more active and vocal in mass-slaughtering humans, and is unreasonable on the level of Gu-Landon (maybe even more). By the end of the game, he's essentially reached Kefka Palazzo-levels of crazy.
Goddamn Bats: Grand Chers and Distortion Field-equipped Battas not only have good evasion rates, but barriers as well. In the case of the former, they possess the "Vital Jump" ability. This renders chain attacks less effective and their "Support Defend" pilot skills much better.
Good Bad Bug: Mazinger Z, Layzner, Yuu Brain and Zeorymer all have less parts slots when upgraded to the Mazinkaiser, New Layzner/Layzner Mark II, Nelly Brain and Great Zeorymer, respectively. Status-enhancing parts like the "Booster" note +1 to mobility before the Mid-Season Upgrade event will automatically be sent back to the player's inventory, but a code in the game's programming also gives the upgraded unit the benefit of having said part permanently crafted to it.
By unlocking Gai during the first playthrough of the game, he returns with double the amount of Pilot Points he is supposed to (a first playthrough-exclusive, however). Another bug related to a first playthrough is if Ahmos Gale is not recruited, his machine will not arrive with upgrades.
Player Punch: Think you can use the same method of keeping Mu La Flaga alive as you did back in Super Robot Wars Alpha 3 (that is, keep Mu in the Mobieus Zero even after he can pilot the Strike Gundam)? NOPE: he'll die just as he did in the TV series.
Stock Footage Failure: Bolt Gundam, some of the Hakkeshu robots, and Great Zeorymer have attacks which sunder the earth beneath their enemy's feet, even if said enemy is in midair or the vacuum of space. Ditto with the late-game explosions visible from space... that are clearly taking place on Earth no matter where you are.
Villain Decay: The Great General of Darkness appears in only two scenarios late in Judgment and only if you pick the right route (it's possible to miss him entirely). In the first of these, he attacks while you're fighting someone else, something the Gradosians and Boazanians have already tried. In the second, the Reclaimers defeat him before the heroes even arrive on the scene. Sure, he puts up a fight, but his late, brief appearance, unoriginal style, and the total failure of his plan just don't convey what he was capable of back in his home series.
Woolseyism: In the original Japanese version, the first two characters speaking in the game's prologue make references to ka no mono. This is a very archaic Japanese phrase that means roughly "that man" or "that person". Since this is almost impossible to get across in English, the translation team decided to refer to the person being referenced as "the Converted".