I reported this bug to the Minecraft bug report website but it ended up being not from Minecraft itself.
Then I tested to see and that was actually the case
Whenever I open my server in vanilla 1.16.2 I don't have any of these complications but when I change it into spigot I start facing them.
The problem being is that items will just start not stacking after some time wether when it's placed in a different container or from someone's inventory to another's.
It also occurs to affect items that are modified with NBT data. For normal items, on the other hand, I couldn't find them being affected by this.

Video provided below for a visual representation of the bug.
its good to note that the item it's demonstrated with isn't the only affected item.