I had this problem a few times. Make sure nothing is preventing the hood from closing. Like a tool or nut you might have forgotten. If not try spraying some WD40 on the hood latch, could be rusted and won't latch forward.
Could your hood release handle under the console still be pulled back? My fox body's handle would always stick and wouldn't let the hood latch until I pushed the handle forward again. Pretty annoying, but I got used to it pretty quick lol. You could also check the little rubber bump stops around the core support, I adjusted mine once literally one turn and they prevented the hood from closing.
Hey guys, I had the same problem tonight except I have a right-off-the-lot 2015 Mustang GT. For the life of me, I could not get the hood to close. I am not sure if this is what V6in was explaining, but I turned the little rubber bumpers 720 degrees so they were a tad shorter. The hood still didn't close with just pressure, but it finally latched when I threw it down from about a foot high - I do see a tiny gap now where the hood sits, but I don't think I had many options here! Now if I can just get rid of the cold brake screeching that wakes up the neighborhood... Ironically, I got rid of my old car for this $40k car for the same reasons.