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The problem with the Y-Combinator is, that it cannot be typed. We have Y = \s.(\x.s(x x))(\x.s(x x)), such that Ys reduces to (\x.s(x x))(\x.s (x x)) which reduces to s((\x.s(x x))(\x.s(x x))) = s Ys, thus, having Ys reducing to all sssss...sYs, which means, Ys is not strongly normalizing - and since all typed lambda terms are strongly normalizing, it cannot be typed (actually, in the same way, no fixpoint combinator can be typed).
Anyway, even strongly typed programming languages like Haskell have recursion, even though mostly through calling the function by its name. In the theory of typed lambda terms, you therefore mostly axiomatically define recursion operators, like R:(a->a)->(a->bool)->a, which applies the first argument to a until (a->bool) gets true (there are a lot of other possibilities, though). Anyway, these cannot be expressed as terms, they must be defined axiomatically.
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