Hello, sorry to hear about this issue! I've heard of this happening for 1 or 2 other people but have had no luck determining the cause yet and have never encountered it myself in all my testing.
There is a secret inventory hack for cases like this, but unfortunately you need to have fixed the roof already in order to access it.
Fortunately, since you're playing on PC, if you send me your save file I can debug it for you and get you that missing rooftile. Just shoot me an email at ghosttimegames@gmail.com
Sorry for the inconvenience!