I have puppeteer, i have puppeteer save file and i have ps+. Will my disc save file work on the ps+ version?

Yes! Some games don't have compatibility between digital and retail but pupeteer does work

This game yes... majority not.

Why is that? Makes no sense why saves aren't compatible.

The saves uses a unique code in PS4... this code is different from Digital to Retail (you can find the Retial code in the box)... unless the game read and convert the save from retail to digital (and vice-versa) it won't work.

Few games do that.

Saves from different regions (EU, UE, JP, ect) have different codes too...US Retail uses BCUS-99999 if I'm not wrong.

Sony should have made Puppeteer a PS4 launch game........... I love that damb game.

so for future reference how do i check this out?

There's no official way, just have to search or ask. Most new games are however.