I'm having a similar issue but it happens right before the denoising step while importing ROI sata. The error appears for only four out of 62 subjects.

ERROR DESCRIPTION:

Error using cat
Dimensions of arrays being concatenated are not consistent.
Error in conn_process (line 804)
covariates=cat(2,covariates.data{defaultcov});
Error in conn_process (line 16)
case 'setup', conn_disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 5743)
else conn_process(processname); ispending=false;
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN20.b
SPM12 + DEM FieldMap MEEGtools imcalc
Matlab v.2019a
project: CONN20.b
storage: 19775.9Gb available
spm @ /labdata/data/fMRI_Toolboxes/SPM/spm12
conn @ /labdata/data/fMRI_Toolboxes/conn20b