jsj, while it's too late to 'unring the bell', the above is correct. Describing proper procedure can help others who may be reading this thread avoid making similar mistakes.
A lot of people enter on tourist visas, marry, and file the I-130/I-485. There are approaches that make it less likely that the USCIS will deem the original entry to have been fraudulent (they're not mind readers, after all); but when the marriage occurs rapidly after entry it can become much more difficult to convince the USCIS that the change of heart about intent to immigrate didn't occur until after entry. I expect that there are forums that discuss various ways to finesse these issues with the USCIS, albeit without any promises of success, but as a legal forum we're more focused on laws and regulations.
Certainly there's a back story, but perhaps not one for which she's directly responsible. She's from Beirut, so the "back story" may be that somebody in her immediate or extended family is directly or peripherally associated with somebody who is on a watch list, is involved in a terrorist organization, or has a name similar to somebody who falls into one of those categories, causing her to fall under a broad umbrella of suspicion during the decade following 9/11.
Planes fly in both directions. An alternative would have been for you fly to Lebanon (or a third country to which both of you could obtain admission) and marry her there, then try to bring her into the U.S. as your spouse.
You've already taken the path of AOS, I-130 and I-485, so the I-539 is not appropriate.Quoting jsj_297

