If you have an item with a custom name, it won't stack with items which have the same custom name and type. This occurs even if you rename an entire stack, then split it; they won't re-combine. For instance, if you have a grass block you rename "Grassy" and a second grass block you also rename "Grassy", they are the same type with the same name, but they won't stack together. Likewise, if you have a stack of 64 grass blocks that you rename "Grassy", then split the stack, the two new stack won't re-combine, either.

This also occurs if you give a player renamed items with commands: same item, same name, no other differences from any old item stack, but they won't stack together.