Spouse visa - with poor immigration history

hi my wife came into the country with the help of an agent in 2005. he told her father he could help her come to the UK and work as a help and he will pay the father £250 per month. after her been abused by her employer (not sexual) she left and stayed with her Uncle who later applyed for EEA dependancy in 2008 that was refused in march 2010. we meet in may 2008 and moved togther in June 2009. got married Isalmic aug 2009. and register in Feb 2011. she went back to her country to apply for spouse visa will there be a problem.
the main problem is that the agent took her passport from her when she came in so we dont have a record for her visa and the immegration officer that interviewed her before she left voluntryly said he cant find her visa record. can she be refused under 320(11).