In the beginning of the series Junior says running away from the authorities right before they're about to be arrested is undignified and embarrassing. However throughout the series we see several mafia running away.
Tony should've promoted Bobby 'Bacala' Baccalieri to management sooner because Tony's uncle, uncle Junior trusted Bobby too. Unlike Christopher, Bobby wasn't a drug addict and alcoholic. Since Bobby is a family member it is highly unlikely he would become an FBI informant.
The layout of the windows in Dr. Melfi's inner room/office is illogical. That is, in an early episode, we see Tony dodge Silvio in the hallway of Melfi's office building. It appears to be a typical medical plaza building with multiple physician's offices on that hallway (e.g. the dentist Silvio was visiting, the office into which Tony ducked, and Dr. Melfi's office which we also see.) We see Melfi's office here in the middle of the hallway, not on the corner of the building. Therefore, the two sets of windows in Melfi's inner office are illogical. The windows in front of Tony (behind Melfi) make sense, as they are in a straight line from the hallway. However, the windows to Tony's right are not possible, as they would be looking into the office of the neighboring physician's office on the hallway.
Silvio is seen smoking in season three and by season six it is revealed that he suffers from asthma. It is highly unlikely he could develop asthma in three to five years. if he had asthma before the series began, he shouldn't be smoking at all, smoking would kill him.
In many instances, characters are seen firing semi-automatic pistols (most commonly Beretta 92s).
These weapons are clearly stage guns, as the pistols are seen firing multiple rounds with no movement of the weapons' slides.