How to substitute players for "Timed Subs" option in game turned on for a team.
Select the brown icon at the top of the screen with the 3 players and the clock to start the sub process.
You will get a screen like the first image below.
If you pick which player to remove from right (LINEUP) column it moves to left (OUT) column and selections from the middle BENCH column move to vacant spots in the LINEUP column.
If you now select "Save" you will likely get the error in the picture above. You need to change the time to be less time remaining than the previous sub time (shown as "Previous" time in upper left). Alternately you can also chose to replace that previous sub if you made a mistake there which by selecting the "Replace" option then touching "Save".
If you are doing a new sub then adjust the time as shown above and press save to add the new sub event.