The Premier League said City had accepted and apologised for the breaches, external, with the fines totalling £1.08m. They have 14 days to pay.
Last season the club were fined £2.09m for delaying 22 matches, and manager Pep Guardiola said he would try and make his team talks shorter.
A Premier League statement said: "Rules relating to kick-offs and restarts help ensure the organisation of the competition is set at the highest possible professional standard and provides certainty to fans and participating clubs.
"It also ensures the broadcast of every Premier League match is kept to schedule."
City are awaiting a verdict on 115 charges of alleged breaches of the Premier League's financial rules.
City were charged and referred to an independent commission in February 2023 following a four-year investigation.
It is alleged City breached its financial rules between 2009 and 2018.
City strongly deny all charges and have said their case is supported by a "comprehensive body of irrefutable evidence".
Manchester City have worked hard to improve their record in this area and say they will continue to do so.
Last season was a difficult one for the team in which they failed to win a major trophy across all competitions and Guardiola would have needed extra moments during preparations to conclude his remarks and relay messages - for this reason, the team have not been sent out on time as required by the Premier League.
But the club did cause fewer delays in the 2024-25 campaign compared to 2023-24 - a 59% reduction - and will be aware of their responsibilities if they are to avoid further sanctions in the future.
Simon Stone
Chief football news reporter
The Premier League's stance is fairly clear. Broadcasters spend billions of pounds for the rights to screen matches and part of the deal is knowing, within reason, when they are likely to end.
Not every eventuality can be factored in as players get injured. But the kick-off time and half-time break are controllable.
City argue it was a difficult season, which is true. But the first breach came during a victory over Southampton in October, when they were still unbeaten, were leading at half-time and made no changes during the interval. Yet they were still two minutes and 10 seconds late back onto the pitch.
The sympathetic assessment is Guardiola and his staff are so wrapped up in the messages they deliver that they forget they are over-running.
The less kind view is that they pay no attention.
