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Feshbach molecules forming a Bose–Einstein condensate (BEC) behave as non-ideal bosonic particles due to their underlying fermionic structure. We study the observable consequences of the fermion exchange interactions in the interference of molecular BECs for entangled-enhanced precision measurements. Our many-body treatment of the molecular condensate is based on an ansatz of composite two-fermion bosons which accounts for all possible fermion exchange correlations present in the system. The Pauli principle acts prohibitively on the particle fluctuations during the interference process leading to a loss of precision in phase estimations. However, we find that, in the regime where molecular dissociations do not jeopardize the interference dynamics, measurements of the phase can still be performed with a precision beyond the classical limit comparable to atomic interferometers. We also show that the effects of Pauli principle increases with the noise of the particle detectors such that molecular interferometers would require more efficient detectors.