It happens everywhere, but here's a very simple hand as an example: Heads-up, SB minraises and BB folds.
Here's the hand in notecaddy test environment.
notecaddy worng stack size.png
You can read in the hand history on the right that the blinds are 10/20 and players have 460 and 1040 chips. But on the left notecaddy thinks that the preflop effective size is somehow 1.15