[PS4] LVL 50 but have 46 Skill Points and loot retrieval system glitched

Just as the title says. Im a lvl 50 Siren, but when I go to respec my skills I only have 46 points when I should have 48. I first noticed this when I was testing out a new build of the character and i didnt have enough points somehow.

Another issue im having is my Loot retrieval in Sanctuary isnt working, period. I farm bosses, dont pick up the loot, but they dont go to sanctuary. When the game first came out it was fine, but now that I reached lvl 50 and lost 2 skill points everything is glitched out.

What do I do to fix these issues? Delete and re-install the game software?