Skyrim had the same issues, you couldn't just store anything anywhere. Been so long since I played only thing I remembered where I stored anything was in my own house chest.

I never had that problem... probably because I just give my settlers .38 ammo and a powerful automatic / semi-automatic pipe rifle. The exception are my guards, I give 'em .308 ammo and powerful combat rifles.

Don't worry OP. This is a lesson we all learn the hard way. Back when I was playing Oblivion (my first real Beth game as I only played a small amount of Morrowind) I stored some treasured items in the bedside drawer at the Archmage's room. Well, I finished the Mages Guild, so all would be okay. I soon found out otherwise.

As Summer has said. Save often and reload to fix any mistake.

Ha! That was sensational.

And so typical of the world that we all have to live in. Lol.