It is definitely not a bug as far as the terraforming mechanism is concerned.  The terraform techs can be applied to tiles with a certain minimum amount of land in the tile.  The really good techs can work with 0% land.  The generation of class 20+ planets seems to result in much fewer tiles of the easier land to water ratios.  That, to me, is where the fault lies. Having a class 20+ planet shouldn't preclude minimum and marginal tiles or even really affect their percentages.  Margins and coastlines would occur regardless of the actual size of the continents.  So, I put this down to a behavior in the planet generation procedures that I consider having unintended consequences on the terraforming process.

The devs seem to think that having a 20+ planet should be considered something to be happy about in the first place, and that wanting full terraforming on top of that is just plain greedy.  They may have a point there.  

However, it would be nice to have terraform techs that can't be used become greyed out with a hover tip that says "no tiles qualify for this tech" or something like that.  It should be a principle that everything the game does or doesn't do. it explains somewhere.

By their mechanics versus narrative logic, "terraforming" is a misnomer.  Our citizens aren't really reshaping the map, just finding ways to utilize the less favorable areas. Utilizing one tile doesn't do anything plus or minus for neighboring tiles. No adjacency bonuses here. For me, that bit of narrative logic breaks down when I can only use a so-called terraforming tech just once. Surely, when I was applying the techniques of Universal Soil Adaptation to make one worthless ocean tile usable, I would have taken notes and been able to duplicate the trick. For all my ocean tiles. But, that is even greedier than your point and therefore I never ever mention it. Ever.

Right.

If you were conquering, then it is probable that, while invading the planet, you destroyed several "sectors", which is what the invasion results screen calls the tiles.  This is different than destroying improvements. Those tiles (sectors) were usable, and probably in use, up until you destroyed them, you vicious tyrant, you.

I've seen plenty of 'floating bonuses' after invasions that destroyed tiles. At least once, I was able to reclaim the resource through a...habiforming?...tech.

There was a mod that let you keep using the Ultimate Terraformer but it i seem to not update anymore. The closest mod we have now probably this one https://forums.galciv3.com/469459