When in a Branch, Main File Constantly Pushes Updates

Whenever we have a branch open from a main file and are doing work, we are constantly getting updates that the branch is different from the main file. This is to be expected, as I am working in the branch, but this is persistent and never goes away. The moment I start making changes in a branch, I am presented with a dialog stating there are changes in the main file, even if it hasn’t been touched. Then if I click Update and Keep Main, I will end up overwriting all of the work that has been done on the branch. Not sure why this is happening, but it is certainly frustrating as it negates the whole point of a branch.