One of the most common mistakes players make is accidentally using high-ranked players when using auto-select to train the other players, and the other is exchanging cards for the tokens. In both cases, having players in the reserve will not stop them from being autoselected! A very expensive common mistake. The game does not let you select players in the main lineups only.
So the 3rd response you got from helpdesk is consistent with the game behaviour.
Pro tip: when training/getting tokens, use filters that hide all ranked-up cards.