So when i loot a crate and only take maybe 4 out of the 9 items in it and leave the rest in it the crate does not reset/respawn. I looted a crate at supermarket the other day and took half of  the items and left the rest there. The crate still had not respawned. How can i fix this?

Drop the remaining items in the crate.

I do see when gathering that lootpiles will despawn in the distance  when they have not been looted at all, i always remove all items from any container (even before recyclers came along) as i noticed years ago that it took those containers longer to despawn/respawn when they were half empty.