I used the Saboteur to destroy a planet structure twice now in two days on the same planet and nothing happened at all. It stated that it worked and the timer for the cool started but the planets population, defense, and attack all stayed the same. I am hoping it does not effect the invasion attempt. I think the player may be inactive... I could use some help.

It's possible that you destroyed something like a soilder's outpost, which only affect invasion def. And that number is displayed nowhere.
How is the current area of the planet? is it at full or have some empty spots?

would be a good idea to record the full list of structure next time just to be sure

The space used is full. So no structures have been removed.

The planet had an Engineered Virus elapse so i dropped a Ion Storm Charge on it and ran the population below 100 from 560 and used the ability. I do not exactly what the statement said but it said it worked. i then went to the colony tab to see what it helped which turned out to be nothing. I then went to the Structures tab to see what structure it roomed and they all were intact and the space used was 63/63

Highlight copies of the Colony and Structures tabs

Colony Tab
6 / 560
Population
Peaked Colony, Hostile, Controller:
Planet Guards Legion Bonus Total
Defenses: 1200 0 0% 1200
Attack: 1400 0 0% 1400
Cloak: 0 0 0% 0


Structures Tab
63 / 63
Space Used
Name Effect Options
Warp Gate Mining: 1, Research: 1, Artifact: 1
Phase Cutter Mining: 1, Attack: 100
Assimilation Locus Mining: 4, Population: 200
Archaic Stasis Cells Population: 200, Invasion Defense: 500
Phase Cutter Mining: 1, Attack: 100
Domain Walker Attack: 600, Defense: 600
Domain Walker Attack: 600, Defense: 600
Star Lifter Mining: 12
Star Lifter Mining: 12
Star Lifter Mining: 12
Extracted Lithovoric Stem Bonus Mining: 10%

Your problem is that none of those buildings are constructable buildings. The saboteur effect only works on buildings that can be constructed; not artifact-based buildings or CTL structures. Domain walkers, stasis cells, and the vast majority of artifacts are immune to the saboteur ability.

Thanks, i was not aware of those limitations. That explains a lot.

well, it would be better if the sab would "not work" instead of fizzle.... from OP it appears that the timer kicked in after~