There are a few glitches that should be worked on. They should at least make everyone aware as far as possible. Or we should list the ones we know of. I added two below that I can think of now.
Bone meal can also only be bought and not sold. Thus the exorbitant price of bone meal vs. bones...
This one is a serious one (I have reported it but I don't know if it has been fixed):
If you sell tools via /sellhand or /sell 5 diamond sword for example it will sell any related enchanted tools as if it is not enchanted if it is in your inventory (this is true even if you don't have the tool selected with /sellhand, like if the selected diamond pickaxe is in slot 7 and you have your god pickaxe in slot 1 and you do /sellhand on slot 7 it takes the diamond pickaxe from slot 1 in anyway). I have lost a god sword and a god pickaxe to each of the methods respectively... :banghead::banghead::banghead:
Now I always clear my inventory before selling stuff. I think renaming the item also helps with this but I'm not going to test it out, lol.