My export doesn't match the timeline in working file

The timeline on my exported file (I exported in Media Encoder) doesn't match the timeline on my After Effect working file. The audio and video are still in sync but there is a specific part of the animation that has to start at 27 seconds and in the export it starts almost at the 28 second mark. I have tried everything! It's a mix of video/type and graphic elements and even the graphic elements arent on time so it can't be the frame rate of the videos.