Just to be sure: Do you open an IDML file or an InDesign indd document?
If IDML, it could be a bug with IDML. If InDesign document, I never heard of such a problem…
What is your exact version of InDesign on what OS platform?
It's Halloween! Surely a poltergeist!
It's an InDesign document, in CC 2015 on a windows 10 PC.
I have never experienced it before, and we use guidelines all the time. Both me and my colleague have this problem on multiple files! She set up the template copying it from one document to 5-6 others, and in all the documents the objects (or guidelines) move about 2mm from time to time. Left one time and right the other, so it stays almost in position, but is slightly off. We line up images of products after these guidelines (making the product line up with the guideline, not the box the image sits in), so a few mm off is surprisingly visible.
Since we are avare of it it isn't the biggest problem, but it still is really annoying. If we forget to double check how the guidelines sits on the page before resizing images and moving objects suddenly half the images are placed differently from the other half and so on..