In my options, I have Unusable Equipment, Low Equipment and Low Consumables set to enabled, and these item categories are getting properly sold as expected.

However, sometimes the gold coin icon doesn't show up in my bag, even thought the item get properly sold when opening merchant window. Furthermore, it also seems some items are getting the gold coin icon while they should not. At least these items with the gold coin showing up wrongly aren't sold upon opening merchant window. So the bug is really only with the display of the gold coin icon.

Here's an example of an item missing the gold coin icon (because its soulbound and low level):

Here's an example of an item that should not have the gold coin icon (because its bind when equipped):

I started investigating the issue, and at least I can confirm that the function IsJunk is returning the proper value for the items mentioned above. It seems to be an issue with the icon frame itself.