What causes ecological damage in Alpha Centauri (Alien Crossfire)?

It would appear that your use of neve gas pods may be the culprit, on the grounds that nerve gas is considered an atrocity. As to your question, though, the Fandom wiki for SMAC says the following under the Causes section on the Ecological damage (SMAC) page:

• It is determined by the number of terraforming enhancements you have built in range of that base, and the number of minerals the base is receiving by any means. Committing atrocities such as the use of nerve gas will cause the planet to attack you, unless the Planetary Council has voted to eliminate the ban on them. The same is true with using planet busters but the damage is more severe.
• If enough boreholes are built, the planet will heat up and melt the ice caps flooding everyone. Voting to launch solar shades helps with this, and you can use formers to raise your land.
• Ecological damage can be altered by making choices in the Social Engineering menu that affect Planet.
• You can also build Base Facilities and Secret Project to help, or plant trees to reduce it.

From the Gamepedia wiki for SMAC, the Ecology page goes into more detail under the Precise Formula section:

The ecological damage formula is complex:

1. For each base total the number of Mines, solar collectors, farms, soil enrichers, roads, mag tubes, Condensers, echelon mirrors, and thermal boreholes. Items in squares which are actually being worked count double.
2. Add an extra +8 for each Borehole, +6 for each Mirror, and +4 for each Condenser.
3. Subract 1 for each Forest.
4. Halve if base has Tree Farm, and Eliminate if also has Hybrid Forest.
5. Divide this value by 8, and reduce by up to 16 plus number of previous damages. Set this number aside.
6. Take the number of minerals produced this turn (but not from Orbit)
7. If result from 5 was reduced by less than 16+#, reduce result 6 by remaining amount.
8. Divide minerals by 1 plus number of Centauri Preserve, Temple of Planet, and Nanoreplicator facilities.
9. Sum the values of (5) and (8), and add +5 for each major atrocity.
10. If Alpha Prime is at perihelion (20 years out of every 80), double your value.

Take the resulting number and compute:

• Ecology% = (ValueFromStep10) * Difficulty * Technologies * (3-PLANET) * LIFE / 300
• Difficulty = Normally 3, but 5 on two highest two difficulty levels.
• Technologies = Number of technologies discovered
• PLANET = Social Engineering PLANET value
• LIFE = Native life level (1-3) from Custom Start