Sometimes a little emory cloth works wonders. Anytime we install a toilet, and it doesn't matter what the brand is, we sand where the bolts drop through.
There have been a few times in the last two thousand toilets, where we removed a flush valve, the part that holds the flapper, and sanded where that fit in too.
Like the statement above from Toto, there could be a small imperfection in the casting.
Sometimes it's just a tiny little speak of a bump that can prevent a seal from working.
Most leaks from tank to bowl, are the flapper.
Most of them last a few years.
I've seen some chemicals mess em up pretty good.
If water is going over the overflow tube, then there may be a "fill valve" repair needed.
That can be as simple as cleaning out small specks of dirt, or replacing the rubber seal.
I will say that of the three thousand Toto toilets I sell every year, I rarely ever find anything wrong.
I can't say that about the other brands I sell.
And if I have a problem with a customers toilet, I handle myself. Toto backs me up very well.