I had the Axe of Whiterun which on my save was an Orcish Axe of Fear with a different name, as well as an actual Orcish Axe of Fear with a bit stronger enchantment. Entering Breezehome, I attempted to use the weapon racks. The Orcish axes both placed at weird angles. The weapon plaque above the front door; both axes were yrotated about 270deg the wrong way. All other weapons in my inventory including daggers worked perfectly.

Also, using the staff of fire ball at the home in Solitude on the weapon rack in the basemant that already has greatswords on it to begin with for some reason causes me damage and duplicates the staves when placing two identical ones.

exact same issue for me. I tried putting a orcish battleaxe on the weapon racks in breezehome yesterday and it kind of places it with the back facing the plaque or rack and the axe itself laying sideways. This happens on both the plaques and racks. I Haven't tested this in other houses yet as I only own breezehome so far in my new character.

some weapons will be placed differently on the weapon racks, doesn't seem to be a big issue. there are a few weapons that will be placed in the opposite direction on weapon plaques as well as angled, including a couple swords. Some weapons can't be placed on weapon racks or plaques, they just spawn and fall to the floor, or 'hover' in mid air (spider control rod is a good one to test that with, easy to retrieve). Ghost Swords seem to vanish if stuck on weapon plaques, sometimes when they are placed on weapon racks.