Physical-layer network coding (PNC) can significantly improve the throughput of wireless communication systems by exploiting signal superimposition at relays. It is practically challenging to achieve symbol alignment in PNC. In this paper, we study the impact of the signal power loss and the inter-symbol-interference (ISI) on the system performance when the symbols are not aligned. We show that when the signal power loss is taken into account during the decoding process, the system performance can be improved significantly. Simulation results also show that by sacrificing spectral efficiency, the PNC system using Gaussian pulses generally achieves higher bit-error-rate (BER) performance than the one using square-root raised-cosine (RRC) pulses when symbol misalignment occurs.