In the places I've worked, there have been either formal or informal processes to deal with persistent lateness. None, as far as I can recall, have involved losing pay for occasional incidents. Where such policies do apply, they tended to be invoked only after the employee had been given the opportunity to make up any lost time and either refused or was unable to do so, and their punctuality had not improved.
In practice, an occasional minor incident was often overlooked completely, especially if it involved some kind of transport difficulty such as a broken down vehicle or an incident on the line. In return for that, most employees were willing to occasionally give something back by staying late for a meeting or by not going home until they had finished a particular task.
When I was a manager myself, my own attitude was pretty relaxed. I know things can happen which aren't the fault of the employer or employee, they just occur. I didn't like it if someone appeared to be taking the proverbial, though, and I would then ask them to take shorter breaks until the time was made up. I don't agree with being strict enough to deduct pay for every little incident of lateness, and I'm lucky to have worked in industries and roles where it didn't have a major effect on service provision. I accept that in some places that isn't the case, but I'd still prefer to see some goodwill being given on both sides.
