I recently restored my ConfigMgr site to a new Server 2016 box. One thing I forgot was to increase the maximum MIF file size. I had the drive where ConfigMgr was installed fill up twice before I figured out what was going on. By default, this is set to 5MB. I would recommend increasing it. The max size available for ConfigMgr is 50MB, so just adding a zero should work.
The MIF size is increased by modifying a registry setting:
“Max MIF Size”
Change it to what works for your environment, but remember that it’s capped at 50MB, so don’t set it any higher than that.