It doesn't matter how long ago this took place. If you bought a skill twice, and it actually deducted the skill points on the back end then there would be 2 duplicate entries for the skill under your steamid in the database. The only situation where it wouldn't save it to the database is if it was down/having issues then server died not allowing the queue of queries to execute. Lets say this was the case, then how would the skill points be deducted from the database? Its not possible. Its very common that it shows you buying them on the client side (within the UI) and showing a deduction of skill points (again on the UI) but only on the client side/UI. Re-logging would of set the UI back to normal.
You know if you buy the same skill twice it makes it go up tier?
I have also just read this topic you created:
Saying your skill points and challenges don't add up which is "proof" something went wrong. I have gone through your skills and added them up which total around 535 skill points. I then calculated all your skill points earned from challenges and it was not above this number. So there is no proof there that you are missing skill points. Also on that topic QA accepted and have confirmed to me it is only client side.