Instead of using paragraph indents, leave a blank line (2 returns) after each paragraph. Each paragraph indent will cost you two character spaces, so be sure to take this into account.
MS Word sometimes leaves funny characters in the document (especially with apostrophes or quotation marks). It's great to write the essay in Word, but just to be on the safe side it's a good idea to save it as a text file and then copy/paste that into the AMCAS app.