To quote the dismissal:

Defendants' motion for judgment of acquittal is based generally on allegations of government misconduct. The alleged misconduct consists of the following: 1) conspiracy to suborn perjury and to cover up said subornation in the case of Louis Moves Camp, a prosecution witness; 2) suppression of an FBI statement exposing the perjury of Alexander David Richards, a prosecution witness; 3) illegal and unconstitutional use of military personnel and material at Wounded Knee and the government's effort to cover up said use; 4) violation of applicable professional, ethical and moral standards; and 5) various other incidents of governmental misconduct. For the reasons given below, this court treats defendants' motion as a motion for dismissal and grants judgment of dismissal.

Suborning perjury is when someone convinces someone else to lie under oath, perjury obviously being to lie in court. People can obviously be charged with a crime for this.

If an attorney does it they can lose their license.

Basically what the above is stating is that the prosecution, at the least:

1. Allowed (if not outright encouraged) a witness to lie.

2. Hid evidence that would contradict the lie.

Furthermore, point three references the violation of the federal Posse Comitatus Act (18 U.S.C. § 1385) which severely restricts the government's ability to use military forces in law enforcement in the US.

I am not a lawyer, but generally speaking any one of these offenses could be serious enough to dismiss the case. Essentially, the government so tainted their case, and demonstrated such bad faith, they don't even get a do over (which would have been the result of a mistrial, which was considered in this case).

Points 4 and 5 are rather broad, and could generally speak to the government's conduct, or to specific lesser problems that are not on their own large enough to enumerate.

Source

I'll try to get some more information on the specifics of the dismissal later.

Hopefully someone else can speak to the aftermath.