Their game engines are poorly made, and are typically edited slightly for each franchise. Common elements in all of them include moving/falling platforms sometimes failing to spawn making it impossible to go further (the reason why and how permanent the disappearance is varies depending on the game.) Sometimes levels are unbeatable due to serious glitches which include the incorrect object being set at the end of the level, freezes because of an object error, or the game flat-out crashing (see Pokémon Jade.)
The most commonly used engine started off in Sonic 3D Blast 5 and features very primitive momentum physics. Rings act as health in this game and all other incarnations of this particular game, which are only deducted after the player lands after taking damage. This means the player can get hit with no rings, be flung into some, and not die when they land. The game holds several other bugs like randomly falling through moving platforms and being able to jump off spikes without taking damage. This engine ended up as the basis for most of their other games such as Digimon 02, Mewtwo Strikes Back, and Super Mario 3 Special with slight changes made to the attack mechanics and health system and got revamped in Pokemon Adventure to be (marginally) better.
The second game engine that is far less used is a Megaman engine first seen in Rockman 8. The player can shoot four shots at once, the jump height is much higher than normal, and there's no momentum applied to the controls. Charge shots work but are glitchy, as the boss doesn't show taking visible damage when hit by one (though it still seems to count) and the buster only charges one level, meaning the player can belt out several very quickly. One huge game-breaking glitch causes all objects in a stage to disappear randomly after defeating an enemy, forcing the player to kill as few enemies as humanly possible if they want to avoid this glitch.