After Effects Audio Ahead of Video in Preview and Render
I think you’ve probably identified the cause. I’ve found when using mobile phone footage (And video conference captures) both premiere and after effects can incorrectly identify frame rates. If all the footage is around 59.93-60fps, I would try transcoding it all to 60fps first using a codec suitable for editing (like ProRes), making sure it’s all in sync after transcode, then re inserting it into your project (save a new copy of your project first though).