The mini enemies are incredibly overpowered in higher tiers and difficulties. This has to do with how they are made to be harder to cope with. Minis increase in heath and damage as much as any other enemy as the game goes on, but that makes them incredibly overpowered. In tier 3 in levels like the Creeping Colony and similar levels, you are basically fighting 20 regular tier 2 enemies except cramped into a small corridor which are now faster and harder to avoid, hard to hit and with no loot to compensate for your time AND also re-spawn!
In the basic form, they are supposed to die in one hit and deal only one bar of damage, which I think is the perfect way to keep them. They should not level up higher than that or they basically break levels that should be fun but turn out frustrating.
For one part, minis are more like obstacles, like spikes or missiles are more than enemies. It's the other enemies that make them a treat. Level up other enemies, but don't do so for the mini enemies.
A way to make them tougher in higher tiers without becoming OP, is to make increase how many spawn at the time for higher tiers, but keep them all in the one hit kill, one bar damage area. That way, they are harder to cope with, but not OP. As a group they are tougher, alone they should stay the same.
Consider using a bomb.