Will I have problems later on if I transfer from Saba to AUC (better clinicals)?

You will have to answer more questions and probably lose a couple interviews due to discrimination, but if you prefer to have more options for your clinicals, then it is a give-and-take situation where you will have to choose the better of the two options.

if you are on Dean's list at Saba, then you should be able to do well at AUC.