When analyzing shell casings, there's more than one reference about the fact that it "could be either a Glock or a Beretta". The difference would be readily apparent to an experienced observer. Glock: the firing pin leaves on the primer a distinctive rectangular mark plus, in many cases, the extraction leaves a mark near the mouth of the case. Beretta: they leave just a small mark on the primer left by the percussion pin. There's no way you can mistake a Glock and a Beretta, given a spent casing fired from either pistol.
Numerous times, autopsies are conducted by Ducky, who is wearing the same clothes he wore in the field. Not only does this promote cross-contamination, but it is also highly unsanitary as well as an OSHA violation.
When the scene is towards the team's office windows, a view of the Display Ship Barry, The Anacostia River, and Anacostia can all be seen, and is correct. However at the top of the view is the Rotunda of the US Capitol Building, which is actually north of the Navy Yard and not south like all the other objects seen through the window.
At the end of the opening credits of NCIS when it shows the approach to the US Capitol, the skyline to left of the Capitol dome seems to be a mirrored image. Everything else seems correct but the skyline shows what looks to be two towers (the Masonic Temple maybe?) along the horizon and the building in their immediate vicinity appear to be the same but mirrored.
The approach to the US Capitol is not Washington DC. The Capitol Building is superimposed in another city. There are no smoke stakes near the Capital. The traffic lights in Washington DC do not over hang the streets.
While often the science and technology portrayed in this series (as well as the CSI series, which is also shown on CBS) is accurate or mirrors sound scientific principle, there have been times when methods have led to results simply not possible in the real world.
In an episode of NCIS, the team discusses the difference between ash and maple bats, explaining that ash, while more popular, tend to explode rather than just make a clean break like maple bats. In reality, it's the maple bats that explode, while ash bats make clean breaks.