The assumption with the first sentence is that the apples grew as expected. The assumption with the second sentence is that for some reason, the apples didn't grow, despite your expectation that they would. The second sentence could also merely state that you thought that, regardless of what actually transpired.
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AnonymousI thought apples would grow on the trees by this summer.To my ear, the summer is still on its way. To me it says something like I'm hoping that eventually we'll get apples on these trees; it seems possible to me that we will.
AnonymousI thought apples would have grown on the trees by this summer.To my ear,