The phonecall scene

I've looked through a few analyses of the movie to answer that question, and the consensus seems to be that it was an attempt at humor and/or an attempt to make the Zone even more ambiguous (as it may or may not be connected to the real world in some way).

I can't help but feel that there was some more significance to it, however. Professor announces over the phone that he's on the threshold of discovering The Room, and his colleague violently reacts to this declaration.

I interpreted it this way: For Professor and those like him, The Room represents discovery of the unknown. If Professor were to actually discover all there is to know (think Theory of Everything), he would receive his Nobel prize, but science as an endeavor would no longer be needed, and his Nobel prize would be a useless relic ("just like that telephone"). People--especially those whose spend their lives seeking answers--need mystery.

I think the phone call scene was quite funny - as the man first answers the phone and only then realizes that there cannot be any working phone in the Zone. And it also adds to the mystery of the Zone as it makes it really unclear how the Zone affects the human technology.

Another fine attempt at humor was at the beginning when the man goes to the bar to have a drink, the Stalker says "No alcohol!", and the man says "Well, beer then". :)