I have seen a problem like that, but it happens with Models Collisions, my situation (a rare one):
I set the Moon (3,600,000m Diameter) to collide the Earth (12,400,000m), however in exchange of colliding both dissapear, the model can be targetted but it's not there.......
I think that was a problem that I caused because of the Hi-Amounts of Coordinates, but it seems to not be then.......
If I order the Moon to collide my Ship (Kamikaze), the Moon 1st goes through me (rare not), but when it does a full loop, that time, yes it Collides me, and of course kills me.......
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It isn't related to a Mass Limit problem, both the Earth and Moon I made have Mass set to 2000..........(my models aren't set to "no_collide" and "navbouy", so are really like any other ship)