I have this problem with a ps2tops4 pkg name Psychonauts I have downloaded somewhere as well. The size is ~3GB. On ps4, it shows ~ 60GB taken but it actually uses ~3GB. Don't worry.
I've rebuilt the game from original ps2 iso with PS2-FPKG (v0.6) later and it shows actual space of the game. I guess there are some problems/errors/patches/mods added while uploader building the pkg. Maybe this happens to your pkgs as well.
You can verify this by uninstalling both games and see the actual free space is claimed back.