I had K-1 visa but I married after the 90 days. Can I still have my resident?

What was the reason given for the denial of your residency application? Of course, it is always a bad idea to not comply with the requirements given by immigration, such as not getting married in the requisite time. However, if you can explain the reasons as to why you did not get married, perhaps immigration would make an exception. What is sure is that during your overstay of the visa, plus the waiting time for the petition, you were not in lawful status and could have accrued a 1-10 year bar to admission, if you leave the United States. Did you have an attorney helping you through the process? If not, you should immediately seek the help of an experienced attorney and see if the denial decision can be appealed or what can be done. If you did have an attorney, see if he/she will do the same.

Depends on the reasons for the denial. You need to retain an experienced immigration lawyer to review all the facts, advise you, and handle the case.