One of the great dangers one faces in History of Philosophy is the identification and correction of imaginary flaws. Malebranche is a good case in point. Many of Malebranche's conclusions are obviously wrong. But I think people make the mistake of assuming that because the conclusions are obviously wrong, the reason he was led astray must be equally obvious; and this, I think, is almost universally false. When Malebranche comes to an untenable conclusion, the error is always a very subtle one. But because people assume that the flaw must be an obvious one, they leap on just about anything that doesn't immediately seem right. Many positions Malebranche puts forward that seem at first to be implausible are actually quite plausible in context, given other things he holds; if you bay at the first apparent implausibility, you're off on the wrong trail. The result is that people are constantly proposing as problems for Malebranche things that really aren't problems for him at all; and then other people have to come through and point out that if you read a bit more widely, and place the issue a bit more carefully in its context, the supposed problem evaporates. The flaw is a figment of one's manner of reading. So a major question is: How does one avoid getting mired down in imaginary flaws?
I don't know the answer; but, on the plus side, knowing that it's a serious issue seems like a good start.