As the title says used a Bio Vap and it had no effect, then used another to see if it would do the same but it worked. I know the owner didn't pod as it was an inactive owner. Has anyone else experienced this?

Yup, if someone else used an art or attacked while you hit it with a Bio vap...it doesn't work. It is kind of like the extra damage on bases/NPCs but uses of artifacts. Lovely ain't it?

I was the only person attacking it and I hadn't alerted it.

did you use the biovap before lowering the pop at all?

I did

probably a variation of a common glitch then.
it will often happen where the first hit on a planets pop doesnt actually register

The same thing has happened to me before.

What I believe is the cause is related to the way most counters (energy, shields, hull and planet population) in the game work is that the counter is not sync'ed to the max value unless you do something to cause the game to sync it - you can see this pretty much any time you use a shield amp after you haven't done anything but have been on full shields for ages; or when you unequip an energy-deducting weapon when you are on full energy but haven't spent any for a while.

So for the planet, its hidden pop counter has been merrily growing for weeks or months and has probably reached 10x the actual max population - but it doesn't get sync'ed back down to the max pop until you hit it. So the Bio-Vap halved the hidden value but was still way higher than the planet max pop so it didn't register.

Solution = always tap the planet at least once to sync the population before using the Bio-Vap.

I have done this since it first happened to me and I have had no further problems