Wasn't the tunnel a straight path, how did they get separated, or are there small rooms or even stations with entrances and exits?
I think it's a subway tunnel: more or less straight, but with stairs up to the surface streets at each train station. So, even after the tunnel was completely cleared out, there's always a risk that a zombie will randomly come down the stairs.
Protag-kun left the group briefly to call in transport, presumably unable to get a signal underground and not wanting to expose the group to surface risks by bringing them with him to make the call.