It seems to be a bug:

Error in conn_batch (line 897)
CONN_x.Setup.l2covariates.values{nsub}{nl2covariates}=batch.Results.between_subjects.effects{neffect}(nsub);

Per the conn_batch documentation, there is normally no between_subjects.effects, it's either batch.Results.subjects.effects (no between) or between_subjects.contrast .

If you replace batch.Results.between_subjects.effects{neffect}{nsub}; by batch.Results.subjects.effects{neffect}{nsub}; in conn_batch.m line 897, does it work better?