TBH I don't think it is explained anywhere in the game or even in manual. So can be confusing.

One piece of advice that's also not obvious but will make your game experience immensely more pleasant: buy "keyring" from the woman merchant ASAP. It can store infinite number of keys (you then use just keyring on doors and when right key is present they'll open automatically) which is huge quality of life improvement over dealing with them manually.

Yep, already got it! If only all the keys were being combined with it, automatically