The 49% damage happens because Pokemon's damage calculator rounds down. If your Pokemon has an odd amount of HP, percentage-based calculations involving a multiple of 2 will always do a tiny bit less damage than they are supposed to.

For example, if you were running 0 EVs and 31 IVs, Azumarill's maximum HP would have been 341. 50% of 341 is 170.5, but because the calculator rounds down, Azumarill only loses 170 HP, which is half a point short of 50%. Thus the HP loss is reported as 49% and the Sitrus Berry does not activate.

This is an important mechanic to be aware of due to Stealth Rock. For example, you should always run an odd amount of HP on Charizard-Y so it can switch into rocks three times instead of two.