The directed self-assembly (DSA) of block copolymers offers an attractive route to produce one-dimensional rows of cylindrical similar to 10 nm scale contact holes for lithography. The success of DSA as a viable lithography technique hinges however on the ability to produce cylinders at target locations, with a minimal placement error. Attempts at fundamental understanding of placement error and center-to-center distance variations in the self-assembly process must therefore go beyond a mean-field-based description and incorporate thermal fluctutations. In this study, we use a LandauPeierls-type approach to build a simple model to investigate the effects of thermal fluctuations on the registration of one-dimensional (1D) arrays of cylinders. We also conduct experimental measurements of the placement of contact holes and compare our results to the model. Similar to reported LandauPeierls instabilities in 1D crystals, collective vibrational modes, or phonons, induce large deviations of the cylinders from their equilibrium distribution and can dramatically disrupt the periodicity of the structure as longer arrays are formed.