Are you a US Citizen? Yes, if she gets denied for an AOS, the time between when she went out of status will possibly count against her. But frankly, she's in trouble anyhow if they turn her down. The fact that she is married to a US resident is going to cause issues with other non-immigrant visa/visits.
Note, that regardless of what her I-20 stays, if she withdraws from the program that she was in, she's out of status IMMEDIATELY. Probably her best bet would be to continue her studies if she thinks that there's some reason the AOS isn't going to be approved.

