I faced the same issue last week. Salesforce has provided temporary workaround for this.
If you are using the component for SF1, the workaround is to wrap your component inside a flexipage. When the component utilized the Lightning App Builder as a wrapper, there are no issues with scrolling. To do this, modify your current Lightning Component as follows:
<aura:component implements="force:appHostable" >
<aura:component implements="force:appHostable,flexipage:availableForAllPageTypes" >
and save the changes. From there, create a Flexipage by going to the Lightning App Builder and selecting to create a new Flexipage. With the modifications listed above, you should now see your custom component in the custom component section. Drag the component into the Flexipage. Then save and activate the Flexipage. Once activated, go to the Salesforce1 app, clear the cache and test the Flexipage that you just created
Please find the link to the known issue created. You can select the green box "This Issue Affects me" and you will receive notifications when the doc is updated and when it has been resolved.