After Ward disarms the cowboy but before he points the shotgun at him, there is the clear sound of a pump action shotgun slide being racked. The shotgun in question is a double barrel type, not a pump action.
Quinn at one point lists all the organizations he is hiding from on Malta, because they have no authority there. He also lists the EU. Malta is (at least in our reality) part of the EU.
Prior to the big rig being lifted into the air at the beginning, there is a POV from inside the cab looking at the driver. The image in the side mirror appears to be running in the wrong direction as if the vehicle were in reverse.
At 33:11 in the altered gravity of the laboratory, Dr. Hall is pouring himself a drink. The liquid in the glass shows what direction is down so liquid he's "pouring" is coming from a hose concealed behind the bottle.
What is shown initially as Malta Island is actually Santorini Island in Greece.
An early scene is supposed to take place in Sterling, Colorado. It is obviously filmed in the mountains or foothills at the base of the mountains. Sterling Colorado is in the plains of northeastern Colorado, near Nebraska, hours away from the front range of the Rocky Mountains.
If the "gravitonium" is as rare as it's made out to be, then it must be incredibly valuable and incredibly difficult to replace, which means it would make no sense for Quinn's agents to just leave a large sample of it on site for the SHIELD agents to find.