Most likely your error is due to trying to average files with different frequencies for phase. Please check your input files to make sure they all have the same .sPAC.LowFreqs. Let us know if that doesn't fix the error.
edit: Actually, there was a bug with indices that would explain this. An update is coming soon!
The PAC averaging process has been fixed. However, we're still discussing how to improve the tPAC process itself as none of the options would currently allow to do what I consider the ideal approach: averaging prior to collapsing across frequencies, i.e. comodulograms as you said. But the tPAC process does not save full comodulograms and doesn't currently allow averaging them. https://github.com/brainstorm-tools/brainstorm3/pull/617