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Superconducting-tunnel-junction (STJ) array detectors with an effective sensitive area of 4 mm2 were fabricated for mass spectrometry. An array detector has one hundred Nb/Al/AlOx/Al/Nb junctions with a 200 mum-square sensitive area. The junctions are quasi-horizontally arranged on a 10 mm-square chip. In the course of fabrication processes, we have found that an anomalous nanometer-step structure appears within the junctions located in the outer region of the array detectors at a specific stage of the fabrication processes. The anomalous steps cause an increase of the leakage current from ~5 nA to a few 100 nA. In order to characterize and prevent the step structure formation, we performed structural analyses with atomic force microscopy, interference microscopy, differential interference contrast microscopy, and transmission electron microscopy. Vertical fault and blister formations were identified in the junctions around the periphery of the array arrangement even on a low stress sputtering condition of 40 MPa. In addition, it is reasonable that a horizontal slip in the AlOx barrier layer is induced by a nanoscale plastic deformation, which causes the large increase of the leakage current.