There is a known issue with skill points being displayed as zero. If this happens to you the important thing to know is you did not lose those skills. This is just a display bug and no cause for alarm. To fix this just log out, stand up and stretch, then log back in and all your skills should be displaying as intended.
A permanent solution to this display bug is being investigated so you will not have to see yourself with zero skill points and have that wonderful brief moment of panic that should only be experienced during a carrier hot drop.