I posted this topic a while ago, where some items were "leaking" across linked chests into slots that should be blocked: https://mods.factorio.com/mod/factorissimo-2-notnotmelon/discussion/637aa5d3c2757b81f497a4de

That issue was fixed promptly, but I'm coming across this again in my current game. From the looks of it, the items leaking have one thing in common: They are of the type where a single unit can be divided, e.g. ammo and science packs. A single unit of ammo has that green bar showing how much of the magazine is left, and the science packs have a green bar showing how much of a pack is "remaining". Might help with the debugging.