Running into a problem when rendering

When I try to render my video from After Effects the audio is not synced. I have visuals that go with music and the final render is always not lined up properly. I also have tried using Media Encoder, and while the music is synced, I still have a couple of problems. When I use Media Encoder, some frames end up not in the final video either, and some clips freeze and hold longer than they are supposed to be. Anyone run into this and is there a solution?