I just lost a game were my PG and SG got injuried and they got substituted not by the guard, not by the SF... by the PF and the C.
Now this is an interesting comment, but my question is - who did you have set as the reserves for each position?
In my games, if i don't have a scrub set as a backup, i will set them according to their position appropriateness.
That is, i set my backup SF as the SG reserve and my backup PF as my reserve C and so forth.
ive had it where my starting PG gets injured, and because i play 'strictly follow depth chart', he shuffles the bench according the backups and reserves that ive allocated.
Now in saying all this, ive usually dressed 11 or 12 players, so im able to set these reserve positions with scrubs, but if you only dress 8 or 9 players in your lineup, this tactic is hard to set.
The other point is that sometimes i know the coach will set a SG at PF, when there are few minutes left, to shoot 3's, or he might set a C at SG because you need the rebound, or something like that. So sometimes that does happen and you will end up with out of position players.
I guess what im saying is that, in my experiences, strictly follow depth chart and play 11+ players, and i cant say ive really noticed the issues you have mentioned.