@Cikku,
You didn't set correct conditions for substitution.
E.g. The player you were to sub is not in your starting 11, or you set the same player as a sub in two conditions. That's why only 3 sub could be made.
I tried several times and he only made one substitution during the match.
I also tried with different times, the same thing happens.
All the players are in my lineup.
@Panta
The lineup instructions are still in development, therefore have not been included in the manual. For your specific case, you should choose a time during the match when you want to make the substitutions, and if you don't have a second condition, set it to nothing (grey square).