If you drop items in a hopper which is filled with the renamed item you throw in, it wont stack and the item doesn't fall in the hopper.
Only if all the slots of the hopper all filled with the named item.
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Kumasasa i forgot to mention that it happend only if all the slots were filled with the named item
Cannot reproduce even with that setup.
I reinstalled minecraft and now it's fixed. Must have been a glitch of some sort.
Anyway how do i delete this post?
No need to delete it, it has been resolved.

Can reproduce when quitting and reloading the world --> Duplicate of MC-5413
First: create a stack of renamed items over the anvil.
Second: Split the stack into two or more smaller stacks
Third: Put a hopper on another hopper (facing away from the lower hopper). Block the lower hopper with an redstone torch below it.
Fourth: Put the small stacks inside the upper hopper with leftclick-hold and drag-over.
Fifth: Try to put another smaller stack of the renamed items on the existing renamed items in the hopper.
Result: 90% of trying switches the items in hand with the items in hopper (not stacking, replacing). I'll try to make a video of it.
THAT is the issue, i found. (tried to build a item sort machine with hoppers. check out the tutorials on youtube. the "placeholder"-items (2, 3, 4 and 5 slot) i ever renamed on anvil to prevent accients.)
I hope, my english is good enought for it to reproduce the issue and helps to fix this bug.
Cannot reproduce.
Renamed items do stack in the Hopper, see screenshot.