I am having the same problem. I use AlwaySync as my backup/synchronizer application. OneDrive is changing the Date Created to the moment it was uploaded. The date taken and date modified seem to be left alone. AlwaySync apparently uses the date created and it thinks the files in OneDrive are newer.
To me it does not make sense for OneDrive to change the date created to the date/time when it was uploaded.
For as long as Windows has been around, and back in DOS before that, Date Created has been the date the file was created on that drive. If you set up a new computer, and copy the files from another computer over a network, they will all have Date Created value of the date they where created/added to the new drive.
The Date Modified field will not change in these scenarios. Date Modified SHOULD only change if the user has chosen to change the file. It does appear that Microsoft is making changes to files and then updating the Date Modified field to reflect the date of these changes.
I understand the frustration and desire for these fields to work differently, and agree that MS should not be changing user files (which updates the Date Modified value ) without user consent. However, I would also say that there is a specific field intended to protect against this exact problem: Date Taken. This is the ONLY field that people should be using to store the date a photo was taken. This seems obvious -- what if you crop a photo or remove red-eye or need to rotate and then you save the updated photo? Obviously, the file date fields will reflect the date you saved the changed the photo. But the Date Taken field will still correctly hold the date the picture was taken.
I came here looking for a solution to a related problem, because I also see that Date Taken field has been wiped out on a small % of my photos, all taken with a specific third-party camera app (ProShot on Windows Phone), while they do show the Date Taken correctly on the phone, so somewhere in the transfer the value appears to have been stripped. However most photos even from that app do correctly have a Date Taken value. Fortunately, the number missing Date Taken is only about 1%, nowhere near the 10%-20% the original poster described for changes to the Date Modified field.