Comment 14 for bug 1026063

I had the same problem and I know how annoying it is when using Netbeans. I found a work around for this.

On Ubuntu 14.04.1 LTS, under Settings -> Mouse and TouchPad.

I have:
Disable while typing (checked)
Tap to click (un-checked)
Two finger scroll (checked)
Natural scrolling (unchecked)

The tap to click feature was causing the problem, it seemed on some applications scrolling with two fingers was considered as both click (since it's a tap) and scroll (since it's two fingers). Removing the check for 'tap to click' solved it for me.

Hope this helps.