- the brothers went from complete lack of concern - acted just like innocent men would act - to utter panic, with no preparations whatsoever for their escape (as if it never occurred to them they would have to escape);
- the Official Story of the shooting of MIT Police Officer Sean A. Collier makes no sense ("In Tsarnaev Trial, Prosecutors Turn Hostile Toward Own Witness");
- authorities, using chemical analysis, can't connect the making of the bombs to any place known to be associated with the brothers;
- witnesses who know the brothers and might have provided assistance to the defense have all been killed, deported or arrested;
- "FBI’s ‘Smoking Gun’ Video of Boston Marathon Bombing Doesn’t Exist" "What’s Not Being Revealed in the Tsarnaev Courtroom" The prosecution was consistently dishonest in what was supposed to be a slam-dunk case ("Prosecutorial trickery in US v. Tsarnaev muddies the waters of what should be a straightforward prosecution");
- there are multiple versions of the kidnapping and escape of Dun Meng ("Boston Carjacking Unravels 1" "Boston Carjacking Unravels 2" "Tsarnaev Carjacking Victim’s Escape Video a Microcosm of Why a Closer Look Is Warranted"), a very useful witness as he claims Tamerlan Tsarnaev confessed to both the bombing and the killing of the policeman;
the connections of Tamerlan to the US government and the odd but extensive efforts the US government made to cover this up, including failing to assist in the identification, and thus apprehension, of the suspects ("MIT police officer's statement suggests FBI was watching Tsarnaevs the night Sean Collier was killed"):
"Author and journalist Masha Gessen ponders the question of a cover-up in her book about the case, The Brothers: The Road to an American Tragedy, released on April 7. According to skeptical book reviewer Kevin Canfield, writing for the Kansas City Star:
“Gessen’s thinking goes like this: Because the FBI questioned Tamerlan Tsarnaev in 2011 and monitored him and his family, agents would have been likely to recognize him in surveillance camera images captured at the site of the bombing, which killed three and injured hundreds. Nonetheless, she writes, agents with the FBI’s Joint Terrorism Task Force didn’t initially identify the Tsarnaev brothers.
“A… logical explanation,” Gessen argues, “is that the person or persons who were in a position to recognize the brothers were consciously concealing this fact in order to protect their own or the agency’s reputation—either because it would look like the FBI had fumbled a solid investigative lead, causing tragedy, or worse, because the FBI had considered Tamerlan an informant.”
Even more incendiary is her suggestion that the FBI deliberately kept police at arm’s length as they were pursuing the brothers “because it needed to ensure that no other law enforcement got to Tamerlan Tsarnaev before the FBI had captured—or killed—him. In other words, the explanation that best fits the facts is a cover-up.””
By the way, a lot of these links can't easily be found with a Google search (DuckDuckGo produces quite different search results!).
Added: "Five Key Questions That Were Not Asked During the Trial of “Boston Bomber” Dzhokhar Tsarnaev"