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.

Source: former R4 - haven't refereed in a very long time though.

For the Bournemouth match, I expected much more stoppage time than they gave. I don't think it's a systemic issue, but rather an issue with an individual referee.

EDIT 2: Current time laws from FIFA

Allowance for time lost
Allowance is made by the referee in each half for all time lost in that half through:
• substitutions
• assessment and/or removal of injured players
• wasting time
• disciplinary sanctions
• stoppages for drinks or other medical reasons permitted by competition rules
• any other cause, including any significant delay to a restart (e.g. goal celebrations)

Referees must caution players who delay the restart of play by:
• appearing to take a throw-in but suddenly leaving it to a team-mate to take
• delaying leaving the field of play when being substituted
• excessively delaying a restart
• kicking or carrying the ball away, or provoking a confrontation by deliberately touching the ball after the referee has stopped play
• taking a free kick from the wrong position to force a retake