I've noticed a couple of box scores recently where my player rest hierarchy was completely ignored. In both cases (for different teams), the player I had listed as my starting DH was used as the starter at another position, replacing a fatigued player. A different player was available and listed in my player-rest hierarchy at that position, but that player was not used. Looking back through my support ticket archive, the same thing happened at least a third time, and all three examples involved DH's being used as the replacements.

I'm wondering if other people have noticed the same kind of thing. If not, it might be something to be on the lookout for in your box scores. Every time I have noticed it, a DH was involved. But with only three cases, that could be a coincidence. I'll paste some details from my support tickets below.

For the game:
https://www.whatifsports.com/slb/Boxscore.aspx?gid=31078552&pid=1&pbp=0&tf=1

My Seattle lineup (vs RHP, with DH) had Tim Hulett set as the starting second baseman, but his fatigue entering the game was below his auto-rest setting (99%). Julio Franco is listed as the #1 replacement at 2B in the Player-Rest Hierarchy. He is listed as #1, and all the other entries for second base are left blank. Julio Franco's auto-rest setting is "N/A", so there is no reason he would not be the starting 2B in this game.

Instead, Greg Briley was used as the starting 2B. He is set as my starting DH versus RHP. He is not listed anywhere in my player-rest hierarchy, for any position.. Franco did replace Briley in the 9th inning, as a defensive replacement.

For the game:
https://www.whatifsports.com/slb/Boxscore.aspx?gid=30944010&pid=1&pbp=0&tf=10

This was the first game of inter-league play, so the first time my Atlanta Braves lineup vs RHP w/DH was used. My lineup was set with Geronimo Berroa in LF, and Lee Mazzilli as DH. Berroa was below his player rest settings. The player rest hierarchy for LF listed Albert Belle, then Mark Carreon. Both were rested and available. But Mazzilli was used as the starting LF instead. Mazzilli was not listed anywhere in the player rest hierarchy; he was only listed as the starting DH. Mark Carreon was used as the DH in this game, even though he is in the LF player rest hierarchy.

The response from customer support was that Belle should have been used in LF, but it's impossible to recreate the exact conditions to figure out what happened.

I don't have box scores for my older example, but from the old support ticket, it was also a situation where interleague play (i.e., DH lineups) had just begun. Willie Montanez was set as the starting 1B, with Chris Chambliss as the 1B replacement in the player rest hierarchy. Before interleague play began (before the DH lineups were used), Chambliss had been properly used as the replacement when Montanez was tired. In the DH lineup, Bob Horner was set as DH. In two games where Montanez was tired and Chambliss was rested / available, Bob Horner was used as the starting 1B instead of DH. Tom Paciorek was used as DH, and the rested Chambliss stayed in the dugout.

After noticing this, I moved Chambliss into the starting lineup in order to prevent the same thing from happening again. Those two games were the only ones all season that Horner started at 1B, and the only ones that Paciorek started at DH.