I think the same thing happens to me.
Today, in the friendly match
(10655729), I choose my best player, Manolo Villa Fernández
(2229641) a former small forward of the spanish NT, to start in the bench as a power forward, because he played 48 minutes in the last match.
To fill up a better training I take a not too much young PG, José Gurruchaga
(3005901) (that I don't want to train this week) in the starting five as power forward.
Obviously, the first player is much better than the second one, so in spite of playing with "Depth chart until 4th...", my coach decided to start with Manolo.
Result: my best player is now injuried for two weeks.
Very unlucky but maybe it could be avoid if my own decission were more respected by the coach.
And maybe I'm mistaken but I though that the injuried players appeared in red in the summary during the match but the name of Manolo never changed to red. It's that correct?
In other cases I have suffered similar "unexpected changes" always playing with "Depth chart until 4th" so for me it's very clear that there is a bug around this substitution mode.