What exactly happened? You completed the dangerous mines and the shrine told you cannot use it immediately. OK Then you came back later and used the shrine? If I remember right the mines revert automatically to normal after you do the challenge, and if you wish to turn them dangerous, you go and release the seals.
Did you look at the text at the shrine?
Check again and see what happens.
Fastest way to see whether the mines are dangerous (without going actually in) or not is to go to level 40. Ice - normal state, Moss - dangerous state.