I personally keep my phone in the right and fob in my left pocket to avoid any such problems. I originally started doing that to ensure my car key (well before the keyless fob) would not scratch my phone when I started carrying it around years ago, and it has served me well since.
As Andy says, metallic things like coins can interfere with the signal. Its not a unique problem with the fob, as I can cause my iPhone to loose its bluetooth signal to my Lexus or previous BMW if I put too much stuff over it in my pocket -- it's just the low power technology being used that can be interfered with. To test the theory, some have tried wrapping their fob in foil -- effectively making it invisible to the car. Other devices on top of your fob like your smartphone are no different.