The other big miss came from Google, but again analysts see reason to look past the messy quarter.
Ben Schachter, an analyst at Macquarie Research, attributed the weakness in Google to investor concerns about the 6 percent decline in costs per click, or how much the company gets per click per ad, as well as disappointing partner network revenue.
"We don't think these are fundamental problems," he told CNBC. "There is nothing fundamental that says, 'Let me step back. Maybe I don't want to buy here.' I say, yes, of course we want to buy it. We think it's just getting going."
Cantor Fitzgerald's Youssef Squali is also "not overly concerned" about the deterioration in costs per click. He expects these declines to start to improve and turn positive in 2014.
Schachter also said that Google will figure out how to make more money from mobile advertising over time as users shift from desktop. "You have the Internet available to you more often and on more devices—that's generally a good thing," he said. "Even if you pay less per click, you have the Internet around you all the time so you're clicking more often."
Motorola has also been a big drag on Google's profitability but Evan Wilson of Pacific Crest Securities anticipates "a sharp upward revision in terms of profitability for Motorola in the second half of this year and things will look a lot better in terms of profitability growth."
Schachter expects Google shares to reach $1,175, a 31 percent upside.
—By CNBC's Justin Menza. Follow him on Twitter