If you’re using the template files from the voltera community library, make sure to use photon_template, not photon_template_raw. The _raw files contain drills and hole locations which are unnecessary, since the holes connect directly to pads.
Otherwise, if you need those holes in your design, oversize the drill and pad by about 0.2 mm. This will allow some buffer around the edge of the pad to prevent the probe from missing. Also, make sure that you’re loading the holes file (.txt).
We’ll be releasing a SW update shortly which will be able to address hole probing in a more robust way, and hopefully prevent such issues moving forward.