File or Premiere Pro's fault?

I'm working in the Premiere Pro Beta and I have a video that is very long. I cut the video down into three sections. I had no problems on the first part of the video but I got started on the second part and something very weird is happening.

When I try to edit the video, the audio repeats some portions or it just completely cuts the audio out. But the very weird thing is, when I save and close the project and reopen it, the place in which the repeat or cut out happened is fine again and it happens in a new place. It's been very frustrating trying to edit this because what you think needs cut really doesn't need cut.

Any help would be greatly appreciated.