So I've been playing around with this mod myself, and I've had a grand total of one crash - it came when engaging a fleet of naught but a Dragoon cruiser, standard kit.
Now, I'm flying an Aurora kitted with standard Hurricane MIRV currently, and I know that it does not cause the crash - however, Dragoons come standard fitted with Medium MIRV, the best I can gather is that the specific problem is the second-phase Mid-MIRV. Have to play around with the idea more, funny enough fleets with Dragoons seem very adept at evading me, but hopefully it's a lead.
Edit: I think I may have found it - C:\Program Files\Fractal Softworks\Starfarer\mods\Minimash\data\weapons\proj [or equivalent] appears to be missing the "mirv_medium_warhead.proj" from SF Extended. Replacing it seems to allow the MMIRV to reach its second cycle without issue, while firing without the file there produced the typical null pointer exception at the end of its flight. (Even without a target within range)