I don't know the case well enough to comment on it, but my money would be the same explanation: badly coded automatic discovery systems. The DHS has been caring notoriously little about false positives and I wouldn't be surprised if some obscure rule got triggered because of her mother being on a blacklist for who-knows-what reason either related to her original ban to the lawsuit. The DHS must change because its mixture of incompetence, lack of transparency, and absence of supervision is a recipe disaster, but saying this particular case was made on purpose seems like sensationalist FUD to me. I could be wrong and it might be true, but I think everyone is jumping on conclusions way too fast.

There is no excuse to the government allegedly lying in court, but I have a hard time imagining anyone would do such a stupid move in their right mind. What could one hope to achieve by putting the daughter on the no-fly-list in the first place? That the key witness missing her flight would cause her testimony to be ignored? That stalling the process by a few days would tip the balance in their favor? That the consequences of the plot being discovered (which depended on the Malaysian airline keeping its mouth shut) do not considerably outweigh its benefits? Also noteworthy is that this particular case is an appeal to a first decision back in in February 2012 that the DHS won, for reasons completely unrelated to Dr. Ibrahim being or not being able to board the flight: http://caselaw.findlaw.com/us-9th-circuit/1438741.html