Assumption: Radio waves, microwaves, light... they're all photons. They're all electromagnetic waves. Particles. Waves... Anyway... I'm assuming by "communications" that you mean things between AM radio and the GHz frequencies of Cell Phones — and nothing else. Because if you allow for laser communications (light passing through your atmosphere) there's no way to stop the comms.
Assumption: I'm assuming that you want "natural" solutions and not "technical" solutions. In other words, no aliens broadcasting noise to block the comms. Having said that... huh... That gives me an idea.
Van Allen Radiation Belts
Let's say your planet has a much more dense magnetic field than Earth. The Van Allen Radiation Belts would be much closer to your planet than they are to Earth. All those charged particles could wreak havoc with comms.
Your Planet is an FM Pulsar
Let's put something a bit asymmetrical into your planet's molten core. Maybe a micro-black-hole that hasn't got around to sucking down the entire planet yet. It's working on it! But in the meantime, it's sending out an FM broadband signal somewhat like a pulsar that made landing on the planet itself a doozy... much less communicating with the ship! Oh, and the fillings in your teeth just became magnetized.
Your sun's a bit more energetic than most stars and the result is an over-charged thermosphere. You don't just get Aurora Borealis... you get the Great-Great-Grandmother of All Aurora Borealis! And it comes with lightning storms! Planet-wide! If you thought landing with that honking black hole swimming around in the bowels of your planet was a problem, wait until you're being struck by thousands of lightning strikes a minute! Each one of them producing a mini-EMP.