At the end of last year I applied a PLEX against my unsubscribed Alt account, to allow me to respond to the War Dec which ended up not requiring a response.
Aside throwing some Omega skills into the training queue, I effectively ignored the account for the rest of the month. I assumed after 30 days it would switch back to an Alpha state again.
Half way through February EVEMon started to warn me that I had less than one day training on that Alt account. It appeared that Transport Ship V had continued to train for a dozen odd days after my PLEX had expired.
I logged into the account – was told it was now in an Alpha Clone state, and the last 12 hours of Transport Ship V stopped.
I did a quick search on Google but didn’t find anything conclusive.
I then logged a bug report – but CCP’s response was to close the ticket without comment.
Free SP for me I guess.
Evehermit 
Heh, oops. Years of being subscription only means that there are probably some not often traveled code paths out there.
I am pretty sure CCP doesn’t respond to bug reports, only support tickets. Closing yours could just mean that it is a known issue.
But even if it is a bug, I doubt they are going to remove anyone’s skill points unless they catch you exploiting it en mass.