Using ReplacementBlock on a door causes the original door to drop as an item. For example, if I want a wooden door to be replaced by an acacia door, the wooden door drops as an item and the acacia door is placed. The player now has two doors.

Here is the configuration that I used to discover this issue:
http://pastebin.com/A83irQiL

A smaller issue is that the new door isn't really placed - it also drops as an item.