Not all that surprising he is struggling physically.
He may already be good enough to play in most Liga matches, but you have to keep in mind the lad is still only 16.
Expecting him to make the jump up from Juvenil A, bypassing Barca B altogether and giving him tons of minutes against fully grown men in a top 2 league in the world is rather naive.
Even Mbappe was not given regular minutes with the first team in Ligue 1 until he was around 18.
I understand fans are excited about Fati and his potential, but regardless of how good he is technically he is not physically ready to become a regular in the first team just yet.
No need to ruin the best talent from La Masia in ages. Right now he needs to be the first name on the team sheet for Barca B, get some Spanish NT experience, train with the first team regularly and occasionally be given the odd start or cameo here and there in dead rubbers or against minnows at home.
Do it right.