Yeah. Probably. It's best to not use the home directory for storing stuff in containers. Use a path like
Background: The home directory inside the container will be replaced with the home directory of the user on the host (your laptop or HPC) that runs the container.
-pwas. I thought it was before the Singularity image, but it's after. Can you please paste the whole singularity command here?
singularity exec -B $PWD/Input:/Input -B $PWD/Output:/Output cellprofiler_3.0.0.sif cellprofiler -p /Output/Batch_data2019_05_29.h5 -f 1 -l 1