What's wrong with the Summa Theologica? I've heard that there were two points of Catholic doctrine in Aquinas' Summa Theologica that were later successfully defended to the contrary.  One, I think is the Immaculate Conception of Mary (although I don't know where that is in the Summa) and I'm not sure what the other one is. 

Excluding things that might not exactly measure up to modern science. What are the points of doctrine in the Summa that don't line up with Eternal Law?
There are two types of errors in the Summa. The first are of the type caused by a Medieval understanding of science and biology. The second are actual theological dead ends.

The most famous of both has the first causing the second. Thomas believed that the entirety of the body was in the man's "seed". Because of this he argued that the Virgin Mary was purified from sin in the womb. The current Catholic teaching, of course, is that the purification was at conception.

After that it really does become difficult to say that there are "points of doctrine in the Summa that don't line up with Eternal Law". There are competing perspectives which have been proposed, but that does not mean that that Thomas was wrong, simply that there are other, valid views and vocabulary which have been used to express the same thought.