You are all right and these problems are in the game, but how many of you paid attention to the number of transcendence points? After today's reset, a certain amount may be lost, which will permanently close your last perk (for 100 points).
So in my first chapter the counter displayed 10/30 and in the fourth chapter 15/90. Of course, these missing 25 points were absent from me and did not get reset.
upd. Sry for bad print/ It's my first report.