My wife is having a medical abortion. we had sex immediately after she took mifepristone but before the misoprostol was taken. could she become pregnant again from this encounter?

Since a "medical abortion" is not always successful in ending a pregnancy, obtain a serum HCG test to determine whether the pregnancy is still present. Given the circumstances in your question, if the medications described are taken as prescribed, a "second pregnancy " is highly unlikely. If the HCG test is positive, see your GYN physician for an exam and possible minor surgery (D&C).