Update Brainstorm and you'll get access to a new option "Output configuration: Save average connectivity matrix (one file)" directly in the coherence process options.
However, an error occurred when I conducted paired t test.
This error means that most likely there is no meaningful data in input, but it should be caught earlier and Brainstorm should display a nicer error message than this... Do you also get this when you try with your real data (ie. the real data you want to test)?
Please note that you should probably not be using parametric tests for coherence... For data data is not normally distributed, prefer non-parametric tests:
https://neuroimage.usc.edu/brainstorm/Tutorials/Statistics#Nonparametric_permutation_tests