It's also happening in my save, first time I noticed was season 26/27, started to pay more attention in season 27/28 and the playing time seems randomly assigned.
1 kid with 10(1) apps, for a total of 679 minutes has actual playtime of regular starter
1 kid with 9(5) apps for a total of 822 minutes has actual playtime of breakthrough prospect
post I've made with screenshots: https://www.reddit.com/r/footballmanagergames/comments/1187gyv/another_episode_of_fm23_logics/
I've upload a save: "Playing Time Bug", players are: Joan Miquel Tribulietx (breakthrough) and Marcus Vinicius (regular starter)
Please look into it, it's very frustrating.