It should be more logical to think of the portal going rogue as MC new actions changing how other adventurers would have behaved and then that someone MC interracted wth not killing monsters inside, hence it flooding.
MC having annoyed Oga and the asshole getting a job to investigate the place right after the fight that he refused to do for being in a bad mood make things click.
If portals are appearing in a different order or things changing inside them because of MC actions then the special portals he know that should appear shouldn't actually appear.
The author clearly isn't good at writing the plot, it seems like the corrupt boss sent people in the Ring of Wisdow portal with the intention of killing everybody and secure the object from the start, how could people outside know of it if in the original timeline there was a black ops operation?
Makes us think that MC isn't the only one that returned to the past, but doesn't seems like that from the phone call.
Another thing, MC and the dragon were in contact when the clock sent him back, wouldn't surprise me if the dragon was too.