The implication is that Fox only brought enough for one dose, and that was based directly on Bruce Wayne's own blood chemistry. When it became apparent that they'll need more (much more), Fox goes into town to collect the additional two sample doses, returns to drop them off at the Batcave and then heads back to Wayne Industries to get started on the next batch:
“No, I just want you to know how hard it was. Bottom line, I synthesized an antidote.”
“Could you make more?”
“Planning on gassing yourself again?”
“You know how it is, Mr. Fox. You’re out on the town, looking for kicks . . . someone’s passing around the weaponized hallucinogens . . .”
Fox stood. “I’ll bring you what I have, but the antidote should serve as an inoculation for now.” He nodded to Alfred. “Alfred, always a pleasure. I’ll see myself out.”
FOX: No. I just want you to know how hard it was. Bottom line, I synthesized an antidote.
WAYNE: Could you make more?
FOX: Planning on gassing yourself again?
WAYNE: You know how it is, Mr. Fox … you’re out on the town, looking for kicks … someone’s passing around the weaponized
Fox shakes his head at Wayne, getting up to leave.
FOX: I’ll bring you what I have – but the antidote should serve as inoculation for now. (To Alfred.) Alfred, always a
So the simplest answer to your question; Batman didn't take the antidote to Rachel because he didn't have it yet, and had he waited for Lucius Fox to bring him the extra doses from his lab (at Wayne Industries) before setting off, he would have lost valuable time in rescuing her.