Mojaatit

Make sure to file with all the correct evidence and fees.

And do not send the original marriage certificate. People make that mistake sometimes in haste. Send copies only. 

Filing for AOS by marriage requires sending a copy of the marriage certificate. The marriage certificate would have been dated after her I-94 stamp.
 
@Suss&Camm has provided excellent advice above. The OP did not meet the conditions to AOS via K-1 since he married after the 90 days. However, his wife can still file for AOS as the immediate relative of a USC, but he has to concurrently file an I-130.

Yes. Like I stated above. Resend your application and include a i-130 petition. She's no longer a K1 adjuster. Your wife will adjust status as your spouse so you need a new petition, i-130. She will adjust status like anyone else that got married to a USC and stayed in the US.

Until USCIS have received the application your wife will be out of status, but this overstay will be forgiven for the spouse of a USC once you file to adjust. Don't have her leave the country, cause then you will have to start all over with a CR1 visa petition from abroad and she might not be able to visit during this process due to her overstay. You would also need a waiver for a potential bar in that scenario.

You had the marriage license but not the certificate. The marriage is only registered after the ceremony.