This paper presents an investigation on structural cracking observed in a reinforced concrete (RC) pier cap supporting a prestressed concrete box girder of 13 m span. Unexpected vertical cracks were observed at service loads on the sides directly under the bearings. A site visit revealed that the elastomeric bearings were compressed on one side with loss of contact on the other. The crack width measurements showed a crack width as high as 1 mm at some locations, where the cover provided was found to be 100 mm, more than the proposed cover of 50 mm. A detailed analysis using non-linear finite element analysis (NLFEA) established the reason for cracking as the reduced contact area at the bearings. The wide cracks were due to the unexpected high cover. The safety of the structure at ultimate loads was also checked using NLFEA and the strut and tie method, and is seen that the structure is safe at ultimate loads. © 2021, Springer Nature Singapore Pte Ltd.