The problem arises from how damage is calculated for ships in SEIV. When damage is done to a ship, a random component is selected to recieve it. If the damage isn't enough to destroy it, then the game keeps track of how badly damaged it is and future attacks continue to hit that one particular component until enough damage accumulates for it to be destroyed. If a component is only partially damaged when combat ends, that partial damage is discarded; at the end of combat each component is either "destroyed" or "intact", nothing in between.
As far as I know, each mine detonation is counted as a completely separate "combat" against a ship. This is the key to the colony component invulnerability. Colony components take 200kt of damage capacity to destroy; with low mine/explosive tech levels, a single mine isn't capable of doing that much. So each mine explosion partially damages the colony component, and then the colony component's partial damage is discarded before the next mine detonates. Once mines become powerful enough to do more than 200kt of damage, colony components can be destroyed in a single blow and this problem goes away.
A simple way that comes immediately to mind to correct this is to lower the damage resistance of colony components; change them from
Tonnage Structure := 200
to something like
Tonnage Structure := 100
and they should be fragile enough for any single mine to destroy easily. I don't think this will cause any balance problems, since nobody should be risking colony ships in combat if they can help it anyway (psychotic Rage Collective colony ships excepted, of course)
I may be misremembering something about SEIV's damage system, BTW, so if my suggestion doesn't work it's my bad.
