I think it might be a problem that many games do not really tell you how many ressources you are supposed to have at a certain point. If you waste ressources, usually the only way to find out if that waste was critical would be to continue playing until you find out the hard way, probably losing all progress up to that point.
In boss battles, in many games you usually can usually orient yourself towards the enemies remaining HP (at least a bit, since many bosses tend to become harder during the fight), but when having to manage ressources during dungeons or even entire games, there's usually next to none indication how much you have left to endure with your ressources, which might force players like me to generally spend as few ressources as possible to stay prepared.
Respawn of enemies does not necessary nullify your progress when you can still avoid the monsters. In Ys for example, I usually just ignore all monsters to get to the next checkpoint as save as possible and then fight monsters and return to the checkpoint to make up the lost EXP.
If you make most encounters mandatory or even make the checkpoint unreachable once you entered the dungeon area this would be a different story of course (not that those would be ultimate solutions).