Lerner may have waived her Fifth Amendment right against self-incrimination. Virtually all the commentary I see on this from conservative websites (and from Rep. Issa) is, at the very least, incomplete. Part of the difficulty is that application of the right against self-incrimination before Congress is an undeveloped area of law. I cannot emphasize that enough. We just don't know whether she waived her right against self-incrimination because there is scant judicial guidance on this, and what guidance does exist is contradictory. We can take civil and criminal case law as a guide to self-incrimination before Congress, but the bottom line is that witnesses before Congress can pretty much get away with whatever Congress will let them get away with. There were several missteps here.
First, Issa let Lerner go with a blanket invocation of the Fifth Amendment the first time she came before the committee. Such blanket invocations are foreign to civil and criminal cases, so Issa let congressional procedure deviate from civil and criminal procedure right out the gate. He tried to clean it up later by issuing a statement saying she'd waived the Fifth, but it's unclear whether a court will accept that (again, there's no precedent either way).
Second, Issa eventually tried to remedy this problem and make the congressional procedure more closely conform to case law by calling Lerner back and getting her to invoke the Fifth Amendment to specific questions. Unfortunately, case law provides that a witness may waive the right against self-incrimination in one proceeding, and then invoke it later at a different proceeding on the same subject. So even if Lerner waived the right at the first hearing, it will be tough to argue that she waived it for the second hearing, at least if we're applying civil and criminal case law.
Civil case law has also held that a witness may make exculpatory statements without waiving the Fifth Amendment in the situation where the witness is both compelled to appear (i.e., the testimony is not voluntary) and the witness makes no incriminating statements prior to the waiver. Both of those things appear to be true here, but as I wrote above, this was a congressional proceeding, not a civil trial. The difference may be crucial to resolving whether Lerner waived and there just isn't any judicial guidance on it. My gut is that the courts will simply default to the easiest route and apply their own civil precedent to Congressional proceedings.
Lerner has indicated that a crime occurred. There have been some suggestions that Lerner is "innocent until proven guilty" and that we cannot take a negative inference from her invocation of the Fifth Amendment. This is false. It is entirely appropriate to take a negative inference from someone invoking the Fifth in civil proceedings or before Congress. She had no reason to do so unless she believed a crime had been committed. We can take Lerner at her word when she indicated that she believes a crime had been committed.