Below are some of the reasons, that stops the clock of the game and hence make the game very long.
Fouls:
The clock is stopped upon a foul and the referee goes to the scorer table to report. This takes more than a minute every time a foul occurs.
Timeouts:
Timeouts are given to the teams to catch a breath and analyze the situation. The allowed number of timeouts can vary in different leagues. NBA now allows 7 timeouts to each team. In case of overtime, 2 more timeouts are given to each team. Timeouts can be granted when the ball is dead or the person calling for timeout has the ball possession.
Half time Break:
In four quarters, after the second quarter and in two halves, after the first half, half time break is given for the players to rest and strategize with the couches for the remaining play. They are generally of 15 to 20 minutes. In big matches, there are performances in the half time. The performances can take even more time.
One timeout last 75 seconds and each team has to take at least one timeout in each quarter so that they cannot save much timeouts for the last quarter. In the final 2 minutes of the play. One team can only take maximum of 2 timeouts.
TV Commercials:
In NBA, TV timeouts and commercials breaks are present for the promotion and publicity of the product. The game stops during these commercials unlike other sports. These timeouts are like the timeouts taken by the teams. As every team has to take the timeout in each quarter, that also works as the TV commercial timeout.
Video Referrals:
Like other sports, the video reviews or referrals are taken on doubted decisions. They take a lot of time as they try to make sure that correct decision is given. A single review takes almost 2 to 5 minutes of the viewer time. Its better to have referees looking at the live action on camera and reporting the wrong decisions to the on-field referee. It can save a lot of time and referees cannot be blamed in this way.
Substitutions:
Substitutions take place when the clock stops and referee signals. One team can have as many substitutions as they want. They don’t take much time as compared to other stoppages.
Overtime:
Overtime is given in case of tie which is 5 minutes initially in most leagues and tournaments. But this time can be increased in case there is still tie until one of the team manages to win. This is something that do not happen quite often and if it happens it cannot be avoided as basketball matches cannot be ended on tie.