Two things I noticed in my survival village:
1. A shepherd turned into a jobless villager
2. There were two masons, but only one Stonecutter block

First of all I haven't broken or touched any job site blocks in both of these situations.

1. The shepherd

All I can say about the shepherd one, is that the shepherd disappeared and a jobless villager was walking around the village border far from the center. I'm pretty sure the villagers are safe, so the shepherd couldn't have died and that there were no baby villagers in the village that could've grown up and got lost.

2. Two masons

I used to have only one mason who i also traded with. Now there's another one who I have not traded with. I know that villagers don't lost their profession if they are higher level than Novice and you break their job site, but as I said, I didn't touch it's job site block. What I think happened was that the original mason somehow lost it's job site memory and a  jobless villager then claimed the job site block.

Unfortunately I don't have much proof or idea why it happened and I can't provide information on how to reproduce it. My best guess is that the villager went too far away of it's job site block.