What is the source file and format that you are editing? How was it captured?
Not sure if the following helps you, but just to highlight how this can happen:
I once encountered this maddening issue after I did a screen capture and edited the screen capture clips then produced it. Extra bits of the scene that I had cut out was still in the produced video. Just a few seconds that would throw off the produced video and make it look like a run on.
It turns out my screen capture settings needed to be set to 1 frame as opposed to the default 10 frames or whatever the default was.
Anyway it can be frustrating but keep at it.
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