It's tough to know the exact reason for a secondary, but biotechs are a special breed - their window for reasonable cost for funding isn't always open.
For now, MNTA has solid revenues coming in from M-enox. And although they believe TEVA's Enox won't get approved, they can't be 100% sure. Since they don't want a potential emergency funding issue in the future, they do a small secondary which will keep them liquid until generic Copaxone is approved and marketed (I think worst case is 2014 when TEVA's patents expire). IMHO, that's the reason for their secondary.
Given the stock price reaction, I don't think the mkt sees the placement as a loss of confidence or a change in outlook by mgmt.