Be it a bug or a mishap, here's what happened:
I was playing with another person in 4-1 and we forgot to activate the pillar before we took the boss warp, then the warp inside the boss room. We were now in the Ruins entrance area but the door was still locked (b/c we didn't activate the pillar in Mines). So we took the red warp back to Pioneer 2 and talked to the Principal who informed us we must find out how to open the seal. So my party went back and found the pillar in mines, activated it, went in the boss warp, entered Ruins, then decided we had to go back and talk to the Principal...Tho, the Principal was convinced we didn't open the seal, and we clearly did ...Just to make sure we couldn't enter Ruins before taking the red warp at the ruins entrance, we went back into mines, back in the boss warp, and then into the red warp, then went to the Principal, same thing: he didn't acknowledge we opened the seal.