I just invade a planet with 40 pop, do 20 damage each hit, but it takes three hits for me to get the invasion button. Did I miss this topic already or is it something new?

It's not new, but most of the posts about it are probably pretty old, I even made a thread about it before. Sometimes, even frequently, the second attack on a planet doesn't work, I don't know why and it probably won't be fixed soon, so just keep it in mind if you're low on energy.

I think it might be certain planets even, this isn't my first time taking er and it's happened every time

This is a theory that's problem wrong, but i'll toss it out there anyhow.
Is it possible that instead of the 2nd shot being lost, it is actully between the 1st and 2nd?

You know how virus trap expiration causes the planet to refill the 24 hours of population?
Is it possible that a planet that was at full pop for sometime goes like this:
hit first
refills to full
hit 2nd(but only 1 "set" of dmg is done overall after this, cause it was "healed" in between)
hit normally~

We know the game have retroactive "refill" issues... That virus above mentioned and, from what I heard, E cube on exotic pulsar~ so this might be the cause~

No. I've tested the missing attack on an inactive's planet. Tapped once, caused damage. Closed the screen and reopened (causing an update to status) and the damage was still there. Tapped again, caused damage. Tapped the second time (after reopening), no damage.