For one thing, researchers have been unable to prove that the downloadable Windows executable, built by the TrueCrypt team, can be constructed purely from the published source code, for reasons based on unusual decisions by the developers – as explained by cryptographer Matthew Green
here.
(In short, the Windows binary appears to save a block of unexplained bytes with the encrypted data. Some fear this is a key to a backdoor, which would allow people in-the-know to decrypt the data without the user's password.)