For example, when I first read through the Acq Inc book's adventure, Orrery of the Wanderer, I thought it looked like a helluva lot of fun. But when I sat down and was actually running the first episode, the nonsensical nature of the opening scenario suddenly became glaringly obvious - the 1st level PCs are tasked with tracking down two missing city guards in a series of tunnels beneath Waterdeep. At least one of the guards has made it all the way to the end, and yet there's hardly any evidence of the guards having passed through each encounter ahead of the PCs. As an experienced DM, I was able to add some details (footprints in the dust on the floor, for instance) and determine on the fly that the traps reset themselves or that various monsters only showed up after the guards had gone through. But a new DM might struggle a bit with the whole premise.
When I come across nonsensical stuff like this in the middle of the game, I like to talk to my players about it, and we all have a bit of a laugh.