Trust me, I think critically. Just ask my boss. He'd say I NEVER think experiments are going well.
The water problem didn't occur until after the peas had grown for almost 2 months. They were far beyond the seed stage. Also, the drought affected all the plants equally. Granted this wasn't the original intention of the experiment, but if you changed the experiment to "How does being grown in the presence of music affect peas' ability to tolerate the stress of drought?", it's valid. The only variable (other than positions on the rooftop, which seems negligable since it looked like all the greenhouses were in VFT-worthy full sun) is music.
They acknowledged that their sample size was too small to draw any conclusions, and they didn't show their data so who knows what statistical analysis they did, but other groups have had interesting results with similar experiments: http://www.plantphysiol.org/cgi/reprint/53/4/641.pdf
There's another one, by Cambridge University I believe, that I can't seem to find. I think they used Led Zeppelin as their rock music and an act from Shakespeare's Hamlet as a neutral speaking voice (neither insulting nor praising the plants.) They think maybe the vibrations from the rock/metal music helped keep the soil loose around the roots.
It was interesting at any rate. I'm gonna try it some day! because I'm a nerd!