Did we forget about adding "clay" to the quarry or stone tools area?? or is it that the swamp is interfering with the build of that??
Sometimes features delay possibility to improve resource.
You need Canal Systems tech to build Quarry on tile with Swamp feature.
@Toffer90 can you add information to tooltip saying what tech you need to build improvement X with feature Y on tile?
I'm not sure how standardized it is.
But it seems if improvement removes feature, then you need following techs to build such improvement:
Iron Working - Jungle, Mangrove
Bronze Working - Forests, Bamboo, Cactus
Canal Systems - Swamp, Peat Bog
Slash And Burn - Savanna, Very Tall Grass
Combustion - Ice
Explosives - All Outcrops
Can't be removed: Crater, Tar Pit, Rainwater Basin, Oasis, Floodplains (this one is weird - Nanotech or Transhuman era civ should be able to remove those, or it may be Toffers pedia displaying what shouldn't display).