Premiere renders out the wrong section of the clip to what is actually on the timeline. It's doing this roughly 25% of the time. Possibly related to changing the framerate of footage. It looks like the clip use the new framerate of the file on the timeline but when it comes to rendering, it uses the original framerate. It's very intermitent. Issue could also be related to outputting via Media Encoder as I don't think I've seen this happen yet when exporting directly from Prem.
Another issue which could be related is recently I opened up an older project in the latest version of Prem and all the video files had defaulted back to their original framerate.
by an chance does the source material come from a smartphone or a screen capture? If so, the problem may be that your source has a variable frame rate which can cause unpredictable and intermittent issues. Here's how to diagnose and fix the problem