Crimea is 60% Russian-speakers, 25% or so Ukrainian-speakers, and 15% or so ethnic Tatars. It is fair to assume that most of the ethnic Ukrainians might prefer to be part of Ukraine rather than part of a Russian Federation with zero protection or adoption of their own culture, and Tatars are historically anti-Russian due to the atrocities committed against them during the Soviet era.
Even if you assume that 100% of the Russian-speakers voted to join Russia (which is not guaranteed- a lot of them will have family or cultural ties with the mainland outside of their language), it's extremely difficult to see 97% approval.
As others have pointed out, the last believable poll figures (pre-troubles) on Crimean nationalism had only around 50% of the population for secession. For almost fully half of the population to change their mind in the last 3 months is completely non-credible.
And we shouldn't be surprised. We all know from past experience exactly what effect gun-toting thugs have in the presence of ballot boxes. Even if you're willing to believe there was no "ballot-stuffing" fraud, there's no doubt that it will effect people's confidence to turn up and vote controversially.