In theory, referees take note of times where the ball is out of play for an exceptional period of time. In lower leagues, many referees run two watches - one for tracking normal time, one to track stoppages.

In reality, time wasting is accepted as a part of the professional game and aside from bonafide injuries, and extreme cases (where the referee produces a card for UGC/time wasting), the ref is going to add ~30 seconds for each goal, ~30 seconds to a minute for each sub, and that's more or less it (again, barring actual injuries which tend to be well-tracked).

For the most part, it's a decent formula too.