That could indicate a problem with the timestamps in the source file, or the presence of an "edit" atom (MP4 format thing!) that has an offset introduced into the timestamps of the MP4 file. The only way we would be able to confirm is to look at the source file and see what happened.
Is this happening on lots of your content? Or just a few files? What is the source of those files that are showing this issue?
To have someone on our team take a look at the file, please file a support ticket in the Azure Portal from inside your Media Services account and you will then be able to upload the source file for the support team to take a closer look at.