I don't understand the term "misalignment".Generally, misalignment or rather alignment is checked during installation of pump to avoid undue forces which may occur if the alignment is not proper.Do you mean "thermal displacement" by Mis-alignment?
Because had misalignment occur at pump-piping mating flange during operation, there would be significant leakage at nozzle junction.
Can you elaborate the whole scenario to understand the real problem?
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SJ