We present magnetic stray field measurements performed on a single micro-crystal of the half metallic ferromagnet CrO$_2$, covered by a naturally grown 2,-,5,nm surface layer of antiferromagnetic (AFM) Cr$_2$O$_3$. The temperature variation of the stray field of the micro-crystal measured by micro-Hall magnetometry shows an anomalous increase below $sim$,60,K. We find clear evidence that this behavior is due to the influence of the AFM surface layer, which could not be isolated in the corresponding bulk magnetization data measured using SQUID magnetometry. The distribution of pinning potentials, analyzed from Barkhausen jumps, exhibits a similar temperature dependence. Overall, the results indicate that the surface layer plays a role in defining the potential landscape seen by the domain configuration in the ferromagnetic grain.