How to reproduce:
1. Create a new Unity project
2. In the Editor Preferences 'General' tab check the 'Verify Saving Assets' option
3. Create a new Prefab and enter Prefab Mode
4. Make sure that the 'Auto Save' option is checked.
5. Make any changes to the Prefab(Change Transform values, add Components, etc.)

Expected result: the 'Save Assets' dialog does not pop up after each change to the Prefab
Actual result: the 'Save Assets' dialog pops up after every change to the Prefab

Reproducible with: 2018.3.0b7, 2018.3.0b10, 2019.1.0a6, 2019.1.0a9
Not reproducible with: 2018.3.0b6, 2019.1.0a5

Notes:
A workaround is to uncheck the 'Auto Save' option and save after making all the changes