Has anyone had this experience?

I was saving my points for later then I got the third shard and my points reset to 1.

Sounds like you found a bug grats now \bug in game

sounds like a rare bug if its the case since it is always addiction for me.

I have never heard of this.

Get that reported! though I have have a level up skill point then found a skyshard skillpoint (got my 3rd shard) and ended up with 2 points to spend....so perhaps a localized thing. You SURE you didn't spend it?