Apart from invisible walls, those are more the result of bad programming and testing than bad design. They were talking about bad design elements that are actually part of the game's design (escort missions, randomly generated stages, etc.).
I'm kind of surprised with all the Persona 3 mentions that no one mentioned that Persona 3 is probably the exception to the rule on the randomly-generated dungeon hatred. Despite the floors being randomly generated, none of them are very big, they all follow the same rules, and there's a set boss encounter with a warp point back down to the ground floor for healing every set number of floors (which the game will, usually, tell you). Not to mention a substantially better battle system than any of the mystery dungeon games. Plus, there's a whole other half to the game with the social links that make it so you continually feel like you are getting stronger, even if you aren't dungeon crawling (and the game highly recommends that you don't continually dungeon crawl).
Come to think of it, I think I'm going to put a question about something like that in the mailbag for the next show...