In a nutshell ... Carbon is being removed from the analysis volume. Therefore, its peak intensity will decrease relative to that of other components (which are remaining behind).
A sample introduced from ambient is always covered by hydrocarbons, water and oxides. Ar sputtering removes the topmost surface layer eventually intermixing the sample. For a compound you have to take preferential sputtering into account what means that some constituents are removed quicker then other. After a certain time the composition during sputtering will be stable, but not necessarily reveal the stoichiometry of your sample. If e.g. carbon is only a surface contaminant its signal will decrease together with oxygen from water. In some cases sputtering under a shallow angle might help not to destroy the sample.