You were correct that the USCIS officer was supposed to retain the original Form I-94 in the file. But it could be a mere oversight. This gesture alone may not be an indication that the application could be denied upon a finding of marriage entered for the purpose of evading immigration law. That would depend whether the officer found your statement and evidence to be consistent with a bond fide marriage. Without those details, it is hard to predict which way it will go.
Oliver Huiyue Qiu, Esq.
Mailing Address: P.O. Box 1271, Union, NJ 07083
Office Visit: 5 Penn Plaza, 23rd FL, Manhattan, between 33rd St and 8th Ave (By Appointment)
(646) 820-7658 Mr. Qiu is a co-chair of American Immigration Lawyer Association's New York chapter Federal Practice Committee. This response should not be deemed as the creation of attorney/client relationship. Legal advice should be sought with a competent immigration attorney.