Even it's 1.12.2 version, I think this kind of "bug" is still there in 1.13 or above. Because someone wouldn't notice the inconvenience it gives, because of not everybody used to use these kinds of "function" of Hopper to use for anything, take a look over the picture to see.

Note that the green is not what suppose to happen(So it's bug), in this case, mean "won't get through"

Even me, I see this unexpected function is not used for anything in redstone because it's useless, I'll use another technique of redstone for temporary use until this is fixed

*Pic 6 mean I want to make a fully automation shop trade without using plugin to modify it, but people may give trash, ruin the process, please fix the way hopper should have in pic 3, and I could have the full automation shop in server, when player put in even correct item and trash, the filter process will keep filter and ignore the trash. will never be stuck again

*UPDATED: This bug(or technically itself) is confirmed even with the newest update 1.13.2 or 18w50a.

*UPDATED: This is not a bug, it's the "intentional" function that Mojang is added for no reason.