There were some improprieties found as it relates to the conduct of Amazon's agents and in the RFP process, but it got the greenlight overall. This might be the problem with Amazon litigating the changes to the RFP process. Oracle already litigated the previous version of the RFP. It looks like the process changed in part to head off the perception that it was rigged in favor of Amazon. Now, Amazon alleges that this re-rigging made it rigged out of its favor.
So, it went:
Oracle: "This is rigged for Amazon! These requirements can only be met by Amazon! Also it's unfair that it can only be won by a single entity!"
Judge: "The Pentagon didn't want to have multiple clouds because it would defeat the reason for the project. We didn't find that the RFP was corrupt to the point of breaking the law, but it was definitely sort of corrupt, particularly in the case of the dude who was on the committee creating the RFP while simultaneously selling a startup to Amazon while simultaneously telling the Pentagon that he wasn't breaking the law and telling Amazon he was not breaking the law, but he was totally breaking the law."
This obviously put the Pentagon between the rock of leaving the RFP as-is and being sued again for corruption and the hard place of changing the RFP and being accused of improper political influence. If Trump had avoided taking a public stance on the issue it would have been much better for the Pentagon's situation, as this now creates a situation in which no matter what the Pentagon decided they could be credibly accused of corruption.