(I famously ignore Anti-GTKY
signpostings... but seriously, I want to refute a couple of yerricde
's observations as well as add some of my own).
Inconsistent water is something I've thought about at length (pity me). I guess that it stems from developers wanting their bottomless pits to be more interesting. The other two popular methods are lava and spikes (lava being the run-away favourite in modern games). But I would argue that usually, at least with later examples, there was some feeble attempt at rationalising this. Take Alex Kidd In Shinobi World : on one level, you can swim around freely. On another (the dock) contact with water means death. But notice that the enemies that jump out of the water are wearing full-body wetsuits. Maybe the water is too cold or toxic (it's irrelevant anyway as Alex wouldn't be able to jump back up to the platforms even if he could swim here).
The famous Jet Set Willy problem : games where you respawn immediately over where you died. Usually, the developer remembers to alter this behaviour for bottomless pits (or you'd just die repeatedly). Not always though (guilty : Jet Set Willy ; innocent : Streets Of Rage)
Anti-stockpiling levels : to ensure you don't get loads of 1ups before a particular juncture (e.g. a boss), there will be a short, ludicrously hard level requiring a feat of god-like reflexes just beforehand. (Guilty : Quackshot, Llamatron, Metal Slug 2nd Mission's second bastard evil fucker of a minecart level).
The 'no climbing up' and 'killed by contact' flaws are more a case of limited resources than deliberately inconsistent game worlds, IMHO. Another one that seems popular is that any weapon with a close range effect is unimpeded by walls (so your sword / punch works through platforms). (Guilty : Metal Slug 2nd Mission, loads and loads of others)
Flaws of this kind are alive and well in games today. Severance requires you to complete your entire "climbing up" animation before it deems that you are not still standing on the ground (causing lots of unjust rising acid deaths). It also treats "block" as deflecting blows from any direction (woo, magic shield!). Even the mighty Warren Spector isn't immune. There are areas in Deus Ex that require a lock-pick or multitool to exit (tip : don't quicksave when inside one).
There is a bit of crossover with videogame clichés as well...