Reference based motion correction error: All movies must have the same number of frames

There may be, as described under Particle sets job - limit number of micrographs used - #5 by mmclean.
If you ran Patch CTF Estimation separately for each acquisition session’s data, you could connect

  1. a single session’s Patch CTF Estimation exposures output
  2. the combined particle set

to a Manually Curate Exposures job and, inside the job and without modifying any selection criteria, push the Done button. The Particles Accepted output should contain particles derived from that single session only.