The simplest way to treat mines is to make them hostile to all, but these are Advanced Future Space Mines
TM, not the dumb mines of land warfare. It's easy to link mine targeting to transponders, so as long as you have the right transponder on they won't attack you. But that brings up a question:
do ships use transponders during battle? If not, then there's no such thing as a friendly mine once battle is joined.
I imagine, to keep the mines from blowing each other up too, each mine would have to have a transponder. This wouldn't make them as detectable at the campaign level as you'd think, since transponders only double the range at which something can be detected, and mines would have a short detection range to begin with. But it would make official faction minefields more official and, on the lore side, easier to maintain, since it would be easy to keep tabs on the mines and get in to replace them.
Maybe if mines were deployed without a transponder they might attack each other in combat.
The minefield would also probably degrade much faster at the campaign level than a minefield that has transponders. That might be desirable in some cases, though.