Right-clicking to pick up a jar placed in the world destroys anything it might have had inside. I don't know if there's a way to check if it has something inside, though.

It shouldn't. That is something I specifically tested when creating the jar. Are you sure you just didn't see where the item spawned in the world? Are you sure it didn't go into a different jar?

It was the only jar, tested several times.

Please describe the exact steps to reproduce.

Find some naturally generated clay jars, toss an item in, right-click the jar. I haven't tried with player-placed ones, but that shouldn't matter, should it?

Works perfectly fine for me - tested with ZSS v2.4 and Forge 10.13.4.1558.