It would help to know if you're seeing clips actually shifted in time relative to other clips or if it only seems that way when you preview the timeline and you see some sections of audio & video get out of sync.

If clips are physcially shifting, do you the shift happen a a specific point on the timeline and things go out of sync after that?

That can be caused by normal editing if you're not careful. For example, if you use the Duration tool to change the length of a clip on Track 2, even one that's all by itself and not touching any other clips, all clips to the right of it on all tracks will be shifted by the change in duration you made.

One way to avoid that is to drag the starting/ending edge of the clip to the desired location and release it. A pop-up menu will let you choose what you want all following clips to do.