Amnesty International has submitted a brief in the Bemba case on the proper interpretation of article 28 of the Rome Statute, which codifies the concept of command responsibility: http://www.icc-cpi.int/iccdocs/doc/doc669669.pdf. Several prominent international criminal law experts were involved in its preparation, including Mike Newton, Patty Sellers and Charles Garraway. The big issue seems to be whether there is a requirement of causation, a hypothesis that the brief rejects. In other words, the crime of the commander is failure to exercise effective control over those under his or her command, regardless of whether there is any connection to the crime committed by the subordinates. The Prosecutor has filed a short document essentially endorsing the analysis of Amnesty International: http://www2.icc-cpi.int/iccdocs/doc/doc673528.pdfB.
Although this is certainly correct, in a theoretical sense, the question that then needs to be addressed is whether absent any causal link between the atrocities committed and the negligence of the commander, such a case is sufficiently serious to warrant the attention of the Court. Case law of the International Criminal Tribunal for the former Yugoslavia shows that in the relatively rare cases where offenders are convicted on the basis of command responsibility, the sentences have been relatively low, indicating that they were not of comparable gravity to those involving intentional criminal conduct.
The Prosecutor has declined to prosecute cases of wilful killing (see, for example, his February 2006 statement on Iraq) because the number of victims was not large enough. An explanation as to why a negligent commander, whose troops commit atrocities but where no causal connection is established with the failings of the commander, is of higher than wilful killers would be appreciated. I would be inclined to the view that if it cannot be proven that Bemba actually ordered or otherwise was involved in the direct commission of the crimes, then the Court might direct its attention elsewhere.
This is not to dispute that Bemba may be guilty in accordance with article 28 of the Statute. But maybe his case isn't high enough on the Richter scale of gravity if the Prosecutor can only prove negligence.