I have two layer measurement model (i.e, main construct - subconstruct -measured items) with three main constructs and four to three sub-constructs for each main construct. Again the subconstructs are represented by measured variables. 

I run CFA and SEM for the two layer measurement model. 

I got different factor loadings(i.e., estimates) for the same measured items( also for sub-constructs) in confirmatory factor analysis and structural equal modelling. 

what are the reasons for such differences?

thanks in advance. 

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