Maybe the well known issue with the I2C: unlike AVRs, Sam3x8e has no glitch filtering( e.g. If you have a relay close to your board).
You can use a fast-mode compliant isolator like the PCA9517A. The isolator filters 50ns glitches and increases fall time (or RC filters with 20 ohms series résistors and a 200 pf to ground).