I mean, that the question can't be exactly answered without knowing the circuit and excitation waveform.
As far as I understand, there's a steady-state sine wave superimposed with a pulse transient. Assumed this is a linear circuit without a DC offset signal, then the trivial explanation is that you are too hasty and didn't wait for the initial transient to decline.
P.S.: If the transient is just created by hard switching a sine source, you should be able to reduce it by adjusting the initial phase.