Unfortunately, that's a mysterious bug that has existed since Fallout 3 was released and no matter what we tried we could never find out why or what causes it to happen, so we can't really fix it. We made several attempts and implemented measures to try and prevent that from happening, but it never worked.
It's particularly hard to find the causes for it since it's almost impossible to reproduce, it's a very rare bug that happens to some people but not on every playthrough made by the same person, and can happen once and then never happen again even with the same character and the same save file.
It's a bug that has annoyed us for years, we already tried so many things to reproduce and fix it but still plagues us to this day.
My advice is to save the game in a different slot before entering the Megaton House, just in case.
