I believe you can have up to 4 players out of position before being punished with 20% possession.
And for future to avoid injuries:
1) Have your players' morale high.
2) Upgrade your medical facility.
3) Upgrade your turf in your stadium.
4) Don't set hard training intensity for matches.
5) Don't train players when their condition is lower than 80%.
number 4 is rubbish, i never had player`s on any level and never had SO MANY INJURIES LAST SEASON and i`m fully built