Stuck in Arena after Gate Appeared Late

I was in a T-16 Springs Map with the Serpent Queen (?) boss. The game allowed me to walk through the spot where the arena gate should appear, the boss spawned and I killed it. Afterwards, the gate was in place and I could not click on it to port through back to the map. I tried TPing and returning to see if it would resolve the issue but it did not. This caused me to have to exit the map and reset with a new waystone, losing the mods from the previous map.