I've been irritated by this situation for years.
I did a search and found this problem was highlighted in 2010 yet still persists - "TableNinja counts antes at cash games as additional limpers."
I don't want it to do this, its confusing and makes some of my bet sizes look weird.
Separately I had to register a new account to make this post. My email address was not recognized even though it received a happy birthday message from Table Ninja Forums 2 months ago!