Audio edits were fine until rendered- now the edits are quiet and choppy

Hi everyone!

I had to edit out bed creaking noises from a long video. How I did this was clipping a little section of audio right before the creak and replacing the creak with that audio section. When I was editing it sounded like a smooth transition - no issues. I then rendered the video and each edit sounded ...how do I describe...like that filled audio went quiet..sounds like a quick skip. 

Why did this happen? How do I fix this? 

I also exported the video to see if it would sound different but it doesn't.