The b-value of a b=0 is never really zero due to the imaging gradients. On a Siemens system, the exact b-value is calculated including all the imaging gradients and the cross-terms they might introduce. However, for a b=0 image, it should be pretty small, b=15 seems quite high. Also, there seems to be quite a bit of variation in your b-values (I assume they should be identical?). It might be worth checking that your sequence is doing the right thing (see this old paper on the issue) – main thing to watch out for are non-refocused gradient before the first DW gradient pulse.
In any case, the simplest thing to get around this is to add the appropriate entry in your config file, to set the threshold for what MRtrix3 considers a b=0 volume. I expect setting it to 20 should be sufficient in your case (default is 10).